# Patent

## Title
Vector and utilization of the same

## Abstract

The present invention provides a tool for reducing the time and labor required for obtaining a protein by recombinant expression of a gene in a host.
A vector characterized by having two restriction recognition sequences different in nucleotide sequence both of which are recognized by a first restriction enzyme, one of the restriction recognition sequences comprising a part of a restriction recognition sequence recognized by a second restriction enzyme that is different from the first restriction enzyme, and the other one of the restriction recognition sequences not comprising the part of the restriction recognition sequence recognized by the second restriction enzyme. A method of producing a protein and/or a protein domain, using the above-described vector.

## Background
TECHNICAL FIELD
The present invention relates to a novel vector and use thereof.
BACKGROUND ART
Technology to obtain protein materials by recombinant expression of various gene products simultaneously and in parallel using Escherichia coli is very important in the scientific field of structural proteomics/functional proteomics which is generally called post-genomics.
In order to obtain a protein sample from a gene of interest, conventionally, the gene of interest was amplified by PCR; the resultant PCR product was ligated into a sub-cloning vector, with which a host was transformed; the transformed host was allowed to form single colonies; plasmid was purified from the host derived from each colony; the nucleotide sequence of the plasmid was determined to thereby select those clones in which the gene of interest was inserted. Subsequently, a DNA fragment containing the gene of interest was cleaved out from the selected clone using restriction enzymes; the cleaved DNA fragment was purified and then integrated into a fusion protein expression vector; a host was transformed with the vector; the transformed host was allowed to form single colonies; plasmid was purified from the host derived from each colony; a host bacteria for protein expression was transformed with the purified plasmid to thereby express the protein encoded by the gene of interest. The above-described operations are time-consuming; they require nine days at the quickest. Besides, the step of cleaving DNA fragments containing the gene of interest from the sub-cloning vector using restriction enzymes and the step of purifying the resultant DNA fragments require skill.
DISCLOSURE OF THE INVENTION
Problem for Solution by the Invention
It is an object of the invention to provide a tool for reducing the time and labor required for obtaining a protein by recombinant expression of a gene in a host.
It is another object of the invention to provide a method of producing a protein encoded by a gene using the above-mentioned tool.
Means to Solve the Problem
It is known that most representative enzymes used in PCR, such as Taq DNA polymerase/Tth DNA polymerase, has an activity of a side reaction of adding an extra residue dA to the 3′ end of the amplified DNA product in a template independent manner. Therefore, most of the double-stranded DNA fragments amplified by PCR have a 3′-overhang structure in which one dA residue is added.
When a plasmid vector having a 3′-dT overhang that will form a complementary base pair with dA is prepared and mixed with the PCR-amplified product described above, base pair formation utilizing the one-base overhangs readily occurs. When DNA ligase is added thereto, ligation between the vector and the PCR amplified product occurs. Since DNA ligase does not cause ligation between mismatch-containing DNA ends, it is known that self-ligation of plasmid vector alone without the PCR amplified product hardly occurs.
A method in which an open circular vector having a 3′-dT overhang structure (T-vector) is prepared in advance and then a PCR product is mixed for ligation without restriction enzyme treatment or blunt-ending treatment utilizing the above-described nature is called TA-cloning.
Methods for preparing T-vector are classified into three according to their principles.
The first method uses TdT. TdT (terminal deoxinucleotidyltransferase) is an enzyme which adds any deoxynucleotide to DNA ends in a template independent manner. Therefore, when a plasmid is first digested with a blunt-end restriction enzyme and then treated with TdT in the presence of dTTP, a vector in which one to several dT's are added to its 3′ end can be prepared. However, it seems that no report of T-vector preparation by this method has been made efficiently.
The second method uses the TdT activity of Taq DNA polymerase. As described above, Taq DNA polymerase adds one molecule of dA to the blunt end of DNA in PCR reaction solution. However, when Taq is reacted with the blunt end of DNA in the presence of excessive Mg2+ and in the presence of dTTP alone without other dNTPs, one residue of dT is added to DNA. Therefore, it is possible to prepare T-vector utilizing this nature. Briefly, a vector having one dT added to its 3′ end can be prepared by digesting a plasmid with a blunt-end restriction enzyme and then reacting the digested plasmid with Taq in the presence of dTTP and Mg2+. In this method, it seems that the T-overhang generation efficiency varies remarkably depending on the recognition sequence of the blunt-end restriction enzyme used. EcoRV is used in most of the preparation examples reported so far, whereas it is known that the generation efficiency is low when SmaI is used. Methods for avoiding this are disclosed on the internet.
The third method is a method in which a “cassette” DNA sequence containing two restriction enzyme sites directly generating T-overhangs is designed and digested with a relevant restriction enzyme. As an example in which a restriction enzyme capable of generating a single 3′-T overhang is used in an actual T-vector, use of XcmI, Eam11051 and AhdI is reported. According to this method, the above-described “cassette” DNA sequence containing two restriction enzyme sites is designed and inserted into a plasmid of interest. Then, the plasmid is digested with a relevant restriction enzyme. As a result, an open circular plasmid having a dT-overhang at both ends is prepared. (This time, the present inventors used AhdI to prepare a T-vector. With this method, it is possible to design an open circular plasmid having “asymmetric” dT-overhangs. Besides, almost 100% of the open circular plasmids obtained by this method are expected to have a dT-overhang at both ends. Thus, the plasmid is of extremely high quality.)
However, conventional TA-cloning has a drawback that this method cannot control the orientation of a gene of interest inserted into the vector. As a result, most of those plasmids prepared as T-vector have been mainly applied only as (1) a vector for cloning (or sub-cloning) unknown genes or (2) a vector for cloning genes having novel promoter activity. There have been only a small number of T-vectors which are used for TA-cloning of a region to be expressed as a protein (ORF) into an expression vector directly. In the above-described two uses, the orientation of ORF does not matter. The orientation of ORF only matters when conducting protein expression experiments. (This time, in order to select those plasmids in which a foreign gene (PCR product) is inserted in the proper orientation easily, the present inventors designed a sequence in such a manner that the restriction sequence of restriction enzyme NcoI or NdeI appears only when the foreign gene is inserted in the opposite direction. As a result, it becomes possible to selectively transform only those plasmids which express a fusion protein linked to such as glutathione-5-transferase [GST] in the proper orientation into Escherichia coli.)
Vectors for expressing a foreign gene as a GST fusion protein in E. coli have been commercialized. PGEX series vectors which are provided with protease recognition and cleavage sequence with multicloning site following the coding region of Schistosoma japonicum-derived GST are sold by Amersham Pharmacia Biotech. Because GST-fusion proteins are relatively high in solubility and expressed at high levels in E. coli; the protein can be purified in almost one step when affinity chromatography using glutathione-immobilized carrier (beads) is employed; interactions between a fusion protein of interest immobilized on glutathione beads and its target molecule (protein, nucleic acid, low molecular weight molecule, etc.) can be observed easily (pull-down assay); compared to proteins without tag, functions of GST-fusion proteins are less damaged when immobilized on a measuring chip for molecular interaction experiments by surface plasmon resonance; the vecors of this series are used very widely in biochemistry and molecular biology as an expression vector. The inventors considered it will be very useful to prepare a number of expression systems in parallel, each of which expresses various proteins and protein fragments of various lengths, by modifying the pGEX series vector into a TA-vector.
After the completion of genome projects, in order to identify functional proteins and functional domains of proteins and to apply the results in industries, it has become important to perform both determination of tertiary structures and determination of molecular functions at high speed. For that purpose, it is necessary to obtain protein samples retaining their activities which may be used for a series of experiments in the form of soluble proteins. Generally, when a full-length or a part of a gene encoding a protein derived from human, mammal or plant is expressed in E. coli, the protein often becomes insoluble and makes it very difficult to prepare samples for structural/functional analyses. In such cases, it is known that changing the region/length to be expressed as a protein (this technique is called domain mapping or domainization) or introducing one or several site-specific mutations of amino acids improves the solubility dramatically. The same techniques are also used on a protein obtained as a soluble protein, in the process of preparing NMR samples for determination of its tertiary structure, or in the process of improving its solubility for crystallization or its crystallizing property. Among these processes, the process of obtaining many types of gene fragments in a short period of time and at low cost has become possible to achieve due to advances in PCR and reduced prices of synthesized PCR primers. Therefore, the current technical problems are human and time costs for preparing expression vectors, and methods for promptly discriminating whether the protein of interest is soluble or not. The advantage of using GST-fusion proteins for this purpose is that the following procedures are possible: after separating E. coli extract containing a GST-fusion protein into soluble and insoluble fractions by centrifugation, the amount of the GST-fusion protein can be measured by calorimetric assay utilizing the enzyme activity of GST as an indicator in the mixture of E. coli and crude protein. For example, it is possible to colorimetrically determine the amount of the GST-fusion protein on 96-well plates in parallel and in a short period of time.
Considering what have been described above, the inventors have tried the following.
1. Trial generation of GST-T vector was carried out by the above-described method using “SmaI/Taq”. Although a GST-T vector was obtained, it lacked reproducibility and its efficiency in PCR product sub-cloning was low. Thus, it was not practical.
2. Methods for improving the efficiency when SmaI/Taq are used were obtained from documents on the internet and tested. However, no improvement was recognized.
3. The inventors considered that the nucleotide sequence of the blunt end digested by SmaI may be the reason for the low efficiency, and tested a unique improvement method in which the cohesive end generated by BamHI digestion was blunt-ended with Klenow fragment and then dT is attached with Taq. However, the efficiency was not improved.

4. Strategy was changed to the above-described “method of using a restriction enzyme cassette”. As the restriction enzyme, AhdI was selected.

5. It was found that when AhdI is reacted with antibiotic-resistant plasmids [not only pGEX-2T/pGEX-4T3 (GST-fusion vectors)], the ampicillin resistance gene of the plasmids is cleaved. Then, the inventors modified pGEX-4T3 in which the AhdI restriction site contained in ampicillin resistance gene was mutated by introducing a silent, site-directed mutation. (The sequence of the primer (Anti AhdI) used for the site-directed mutagenesis is shown in SEQ ID NO: 21 of the sequence listing.)

6. An AhdI-linker was prepared. Briefly, using PCR primers of SEQ ID NOS: 22 and 23 and a derivative pET32aPACAP from pET32a (Novagen) as a template, PCR was performed to thereby obtain an approximately 500 bp fragment. This fragment was integrated into an existing TA-vector (this time, pGEM-T from Promega was used) by conventional methods, followed by confirmation of the sequence and amplification of the appropriate clone. A purified plasmid was obtained. Then, the plasmid was digested with BamHI to thereby obtain AhdI linker (approx. 500 bp).

7. A vector to be used as the base for GST-T vector (i.e., TA-vector using GST-fusion) was prepared. Briefly, the mutant of pGEX-4T3 obtained in paragraph 5 above was amplified and digested with BamHI. The AhdI linker obtained in paragraph 6 above was ligated into that BamHI site. Appropriately prepared clones were isolated and amplified. The AhdI linker at this stage has no orientation (the linker may be inserted in either direction).

8. GST-T vector was prepared. Briefly, the vector prepared in paragraph 7 above was digested with AhdI to obtain an open circular plasmid, which was then separated and purified using agarose gel. Since the resultant vector has a 3′-dT overhang, it may be used in conventional TA-cloning.

9. An AhdI linker applicable to NcoI ORF selection was prepared. In NcoI ORF selection, those vectors (e.g., plasmids) having a foreign gene inserted in the opposite orientation are digested when treated with NcoI; and hosts harboring such vectors cannot grow. As a result, only those hosts harboring vectors having a foreign gene inserted in the proper orientation can be selected. The method of preparation of this linker is the same as described in paragraph 6 above except that a combination of SEQ ID NOS: 22 and 24 was used as primers. The sequences of the thus prepared AhdI linker applicable to NcoI ORF selection are shown in SEQ ID NOS: 26 and 27. A DNA strand having the sequence of SEQ ID NO: 26 is associated with a DNA strand having the sequence of SEQ ID NO: 27 to form a double-stranded DNA that is the AhdI linker.

10. dGST-T vector applicable to NcoI ORF selection (directional GST-T vector; this means a GST-T vector capable of selecting the orientation of ORF) was prepared. The method of preparation is the same as described in paragraphs 7 and 8 above. However, at the time of sequence confirmation as described in paragraph 7, those vectors in which the sequence corresponding to the primer sequence of SEQ ID NO: 22 at the fusion site with GST is located proximal to the coding region of GST (GST side) were selected to thereby obtain closed circular vectors to be used as the base for the vector capable of NcoI ORF selection. This closed circular vector was also capable of NdeI ORF selection when the design of PCR primers for amplifying the inserted foreign gene was changed; in NdeI ORF selection, vectors (e.g., plasmids) having a foreign gene inserted in the opposite orientation are digested not with NcoI but with NdeI; hosts harboring such vectors cannot grow; as a result, only those hosts harboring vectors having a foreign gene inserted in the proper orientation can be selected.

The present invention has been achieved based on the above-described experimental procedures and results.
The first invention of the present patent application provides a vector having two restriction recognition sequences different in nucleotide sequence which are recognized by a first restriction enzyme, wherein one of the restriction recognition sequences comprises a part of a restriction recognition sequence recognized by a second restriction enzyme that is different from the first restriction enzyme, and the other one of the first restriction recognition sequences does not comprise the part of the restriction recognition sequence recognized by the second restriction enzyme.
The first restriction enzyme may be a restriction enzyme that produces a 3′-overhang in the digested DNA. As a specific example of the base at the 3′-overhang, thymine may be given.
The first restriction enzyme may be selected from the group consisting of AhdI or an isoschizomer thereof, XcmI or an isoschizomer thereof, or a combination thereof.
When the first restriction enzyme is AhdI or an isoschizomer thereof, it is preferred that one of the two restriction recognition sequences different in nucleotide sequence which are recognized by AhdI be represented by the following sequences (I) and (II), and that the other one be represented by the following sequences (III) and (IV).










5′-GACX1aX2aTX3aX4aGTC-3′
(I)
(SEQ ID NO: 1)



 


3′-CTGX1bX2bAX3bX4bCAG-5′
(II)
(SEQ ID NO: 2)


 


5′-GACX5aX6aAX7aX8aGTC-3′
(III)
(SEQ ID NO: 3)


 


3′-CTGX5bX6bTX7bX8bCAG-5′
(IV)
(SEQ ID NO: 4)






(in sequences (I) to (IV), G is guanine, A is adenine, C is cytosine, and T is thymine;

X1a to X8a and X1b to X8b are each independently any base selected from guanine, adenine, cytosine or thymine; X1a and X1b are bases capable of forming a base pair with each other, X2a and X2b are bases capable of forming a base pair with each other, X3a and X3b are bases capable of forming a base pair with each other, X4a and X4b are bases capable of forming a base pair with each other, X5a and X5b are bases capable of forming a base pair with each other, X6a and X6b are bases capable of forming a base pair with each other, X7a and X7b are bases capable of forming a base pair with each other, X8a and X8b are bases capable of forming a base pair with each other;

sequence CX1aX2aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of the second restriction enzyme;

sequence CX8bX7bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of the second restriction enzyme that is included in sequence CX1aX2aT; and 5′- and 3′-represent the individual termini of the double-stranded DNA.)

When the first restriction enzyme is XcmI or an isoschizomer thereof, it is preferred that one of the two restriction recognition sequences different in nucleotide sequence which are recognized by XcmI be represented by the following sequences (V) and (VI), and that the other one be represented by the following sequences (VII) and (VIII).








(SEQ ID NO: 5)










5′-CCAY1aY2aY3aY4aTY5aY6aY7aY8aTGG-3′
(V)



 








(SEQ ID NO: 6)










3′-GGTY1bY2bY3bY4bAY5bY6bY7bY8bACC-5′
(VI)



 








(SEQ ID NO: 7)










5′-CCAY9aY10aY11aY12aAY13aY14aY15aY16aTGG-3′
(VII)



 








(SEQ ID NO: 8)










3′-GGTY9bY10bY11bY12bTY13bY14bY15bY16bACC-5′
(VIII)







(in sequences (V) to (VIII), G is guanine, A is adenine, C is cytosine, and T is thymine;

Y1a to Y16a and Y1b to Y16b are each independently any base selected from guanine, adenine, cytosine or thymine; Y1a and Y1b are bases capable of forming a base pair with each other, Y2a and Y2b are bases capable of forming a base pair with each other, Y3a and Y3b are bases capable of forming a base pair with each other, Y4a and Y4b are bases capable of forming a base pair with each other, Y5a and Y5b are bases capable of forming a base pair with each other, Y6a and Y6b are bases capable of forming a base pair with each other, Y7a and Y7b are bases capable of forming a base pair with each other, Y8a and Y8b are bases capable of forming a base pair with each other, Y9a and Y9b are bases capable of forming a base pair with each other, Y10a and Y10b are bases capable of forming a base pair with each other, Y11a and Y11b are bases capable of forming a base pair with each other, Y12a and Y12b are bases capable of forming a base pair with each other, Y13a and Y13b are bases capable of forming a base pair with each other, Y14a and Y14b are bases capable of forming a base pair with each other, Y14a and Y14b are bases capable of forming a base pair with each other, Y15a and Y15b are bases capable of forming a base pair with each other, Y16a and Y16b are bases capable of forming a base pair with each other; sequence Y1aY2aY3aY4aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of the second restriction enzyme;

sequence Y16bY15bY14bY13bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of the second restriction enzyme that is included in sequence Y1aY2aY3aY4aT; and

5′- and 3′-represent the individual termini of the double-stranded DNA.)

When the first restriction enzyme is a combination of AhdI or an isoschizomer thereof and XcmI or an isoschizomer thereof, one of the two restriction recognition sequences different in nucleotide sequence which are recognized by the first restriction enzyme may be a restriction recognition sequence recognized by AhdI or the isoschizomer thereof and comprise a part of a recognition restriction sequence recognized by a second restriction enzyme that is different from AhdI or the isoschizomer; and the other one of the two restriction recognition sequences may be a restriction recognition sequence recognized by XcmI or an isoschizomer thereof and not comprise the part of the restriction recognition sequence recognized by the second restriction enzyme. The restriction recognition sequence which is recognized by AhdI or the isoschizomer and comprises a part of a recognition restriction sequence recognized by a second restriction enzyme that is different from AhdI or the isoschizomer is preferably represented by the following sequences (I) and (II). The restriction recognition sequence which is recognized by XcmI or the isoschizomer and does not comprise the part of the recognition restriction sequence recognized by the second restriction enzyme is preferably represented by the following sequences (VII) and (VIII).









5′-GACX1aX2aTX3aX4aGTC-3′
(I)
(SEQ ID NO: 1)


 


3′-CTGX1bX2bAX3bX4bCAG-5′
(II)
(SEQ ID NO: 2)






(in sequences (I) and (II), G is guanine, A is adenine, C is cytosine, and T is thymine;

X1a to X4a and X1b to X4b are each independently any base selected from guanine, adenine, cytosine or thymine; X1a and X1b are bases capable of forming a base pair with each other, X2a and X2b are bases capable of forming a base pair with each other, X3a and X3b are bases capable of forming a base pair with each other, X4a and X4b are bases capable of forming a base pair with each other;

sequence CX1aX2aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of the second restriction enzyme; and

5′- and 3′-represent the individual termini of the double-stranded DNA.)








(SEQ ID NO: 7)








5′-CCAY9aY10aY11aY12aAY13aY14aY15aY16aTGG-3′
(VII)


 







(SEQ ID NO: 8)








3′-GGTY9bY10bY11bY12bTY13bY14bY15bY16bACC-5′
(VIII)






(in sequences (VII) and (VIII), G is guanine, A is adenine, C is cytosine, and T is thymine;

Y9a to Y16a an Y9b to Y16b are each independently any base selected from guanine, adenine, cytosine or thymine; Y9a and Y9b are bases capable of forming a base pair with each other, Y10a and Y10b are bases capable of forming a base pair with each other, Y11a and Y11b are bases capable of forming a base pair with each other, Y12a and Y12b are bases capable of forming a base pair with each other, Y13a and Y13b are bases capable of forming a base pair with each other, Y14a and Y14b are bases capable of forming a base pair with each other, Y15a and Y15b are bases capable of forming a base pair with each other, Y16a and Y16b are bases capable of forming a base pair with each other; and

sequence Y16bY15bY14bY13bT is a nucleotide sequence not comprising the part of the restriction recognition sequence of the second restriction enzyme that is included in sequence CX1aX2aT; and 5′- and 3′-represent the individual termini of the double-stranded DNA.)

When the first restriction enzyme is selected from the group consisting of AhdI or an isoschizomer thereof, XcmI or an isoschizomer thereof, or a combination thereof, the second restriction enzyme is preferably selected from the group consisting of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV and their isoschizomers.
When the first restriction enzyme is XcmI or an isoschizomer thereof, the second restriction enzyme is preferably selected from the group consisting of AflIII, BspLU11I, NspI, SphI, BspHI, BsaAI, PmaCI, SnaBI, NspBII, PvuII, BanII, HgiAI, SacI and their isoschizomers.
The two restriction recognition sequences different in nucleotide sequence which are recognized by the first restriction enzyme may be inserted into the multicloning site of the vector.
When the first restriction enzyme is AhdI or an isoschizomer thereof, it is preferred that a double-stranded DNA represented by the following sequences (IX) and (X) be inserted into the multicloning site.







(SEQ ID NO: 9)


5′-GACX1aX2aTX3aX4aGTC-N1-GACX5aX6aAX7aX8aGTC-3′


(IX)


 


(SEQ ID NO: 10)


3′-CTGX1bX2bAX3bX4bCAG-N2-CTGX5bX6bTX7bX8bCAG-5′


(X)






(in sequences (IX) and (X), G is guanine, A is adenine, C is cytosine, and T is thymine;

X1a to X8a and X1b to X8b are each independently any base selected from guanine, adenine, cytosine or thymine; X1a and X1b are bases capable of forming a base pair with each other, X2a and X2b are bases capable of forming a base pair with each other, X3a and X3b are bases capable of forming a base pair with each other, X4a and X4b are bases capable of forming a base pair with each other, X5a and X5b are bases capable of forming a base pair with each other, X6a and X6b are bases capable of forming a base pair with each other, X7a and X7b are bases capable of forming a base pair with each other, X8a and X8b are bases capable of forming a base pair with each other;

sequence CX1aX2aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of the second restriction enzyme;

sequence CX8bX7bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of the second restriction enzyme that is included in sequence CX1aX2aT;

5′- and 3′-represent the individual termini of the double-stranded DNA;

N1 may not exist, and when it exists it is any nucleotide sequence having 1-1000 bases; and

N2 may not exist, and when it exists it is a nucleotide sequence complementary to the nucleotide sequence of N1.)

When the first restriction enzyme is XcmI or an isoschizomer thereof, it is preferred that a double-stranded DNA represented by the following sequences (XI) and (XII) be inserted into the multicloning site.







(SEQ ID NO: 11)








5′-CCAY1aY2aY3aY4aTY5aY6aY7aY8aTGG-N1-
(XI)


CCAY9aY10aY11aY12aAY13aY14aY15aY16aTGG-3′



 







(SEQ ID NO: 12)








3′-GGTY1bY2bY3bY4bAY5bY6bY7bY8bACC-N2-
(XII)


GGTY9bY10bY11bY12bTY13bY14bY15bY16bACC-5′







(in sequences (XI) and (XII), G is guanine, A is adenine, C is cytosine, and T is thymine;

Y1a to Y16a and Y1b to Y16b are each independently any base selected from guanine, adenine, cytosine or thymine; Y1a and Y1b are bases capable of forming a base pair with each other, Y2a and Y2b are bases capable of forming a base pair with each other, Y3a and Y3b are bases capable of forming a base pair with each other, Y4a and Y4b are bases capable of forming a base pair with each other, Y5a and Y5b are bases capable of forming a base pair with each other, Y6a and Y6b are bases capable of forming a base pair with each other, Y7a and Y7b are bases capable of forming a base pair with each other, Y8a and Y8b are bases capable of forming a base pair with each other, Y9a and Y9b are bases capable of forming a base pair with each other, Y10a and Y10b are bases capable of forming a base pair with each other, Y11a and Y11b are bases capable of forming a base pair with each other, Y12a and Y12b are bases capable of forming a base pair with each other, Y13a and Y13b are bases capable of forming a base pair with each other, Y14a and Y14b are bases capable of forming a base pair with each other, Y15a and Y15b are bases capable of forming a base pair with each other, Y16a and Y16b are bases capable of forming a base pair with each other sequence Y1aY2aY3aY4aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of the second restriction enzyme;

sequence Y16bY15bY14bY13bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of the second restriction enzyme that is included in sequence Y1aY2aY3aY4aT;

5′ and 3′-represent the individual termini of the double-stranded DNA;

N1 may not exist, and when it exists it is any nucleotide sequence having 1-1000 bases; and

N2 may not exist, and when it exists it is a nucleotide sequence complementary to the nucleotide sequence of N1.)

When the first restriction enzyme is a combination of AhdI or an isoschizomer thereof and XcmI or an isoschizomer thereof, it is preferred that a double-stranded DNA represented by the following sequences (XIII) and (XIV) be inserted in the multicloning site.







(SEQ ID NO: 13)








5′-GACX1aX2aTX3aX4aGTC-N1-
(XIII)


CCAY9aY10aY11aY12aAY13aY14aY15aY16aTGG-3′



 







(SEQ ID NO: 14)








3′-CTGX1bX2bAX3bX4bCAG-N2-
(XIV)


GGTY9bY10bY11bY12bTY13bY14bY15bY16bACC-5′







(in sequences (XIII) and (XIV), G is guanine, A is adenine, C is cytosine, and T is thymine;

X1a to X4a and X1b to X4b are each independently any base selected from guanine, adenine, cytosine or thymine; X1a and X1b are bases capable of forming a base pair with each other, X2a and X2b are bases capable of forming a base pair with each other, X3a and X3b are bases capable of forming a base pair with each other, X4a and X4b are bases capable of forming a base pair with each other;

Y9a to Y16a and Y9b to Y16b are each independently any base selected from guanine, adenine, cytosine or thymine; Y9a and Y9b are bases capable of forming a base pair with each other, Y10a and Y10b are bases capable of forming a base pair with each other, Y11a and Y11b are bases capable of forming a base pair with each other, Y12a and Y12b are bases capable of forming a base pair with each other, Y13a and Y13b are bases capable of forming a base pair with each other, Y14a and Y14b are bases capable of forming a base pair with each other, Y15a and Y15b are bases capable of forming a base pair with each other, Y16a and Y16b are bases capable of forming a base pair with each other; sequence CX1aX2aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of the second restriction enzyme;

sequence Y16bY1bY14bY13bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of the second restriction enzyme that is included in sequence CX1aX2aT;

5′- and 3′-represent the individual termini of the double-stranded DNA;

N1 may not exist, and when it exists it is any nucleotide sequence having 1-1000 bases; and

N2 may not exist, and when it exists it is a nucleotide sequence complementary to the nucleotide sequence of N1.)

In sequences (IX) to (XIV), N1 may be, for example, a sequence from a derivative which has been prepared by introducing a gene (e.g., thioredoxin gene) and an artificial gene (e.g., PACAP) into an appropriate restriction enzyme site of a commercial vector (such as pET21b or pET32a). It may be preferred that a part of the N1 sequence comprise the second restriction enzyme site. In such a case, even when the purification of the open circular vector that is obtained by treating the vector of the present invention (hereinafter, sometimes referred to as the “PRESAT-vector”) with the first restriction enzyme (hereinafter, sometimes referred to as the “open circular PRESAT-vector”) is incomplete, “empty” PRESAT-vectors generating therefrom by self-ligation are cleaved by the second restriction enzyme digestion and, thus, do not form colonies after ORF selection. Therefore, even when the purification of the open circular PRESAT-vector is incomplete, an advantage that background is very low remains.
As a specific example of N1, the following sequence may be given.









5′-CACCTGACTGACGACAGTTTTGACACGGATGTACTCAAAGCGGACGGGGCGATCCTCGT
(SEQ ID NO: 55)



 


CGATTTCTGGGCAGAGTGGTGCGGTCCGTGCAAAATGATCGCCCCGATTCTGGATGAAATCG



 


CTGACGAATATCAGGGCAAACTGACCGTTGCAAAACTGAACATCGATCAAAACCCTGGCACT



 


GCGCCGAAATATGGCATCCGTGGTATCCCGACTCTGCTGCTGTTCAAAAACGGTGAAGTGGC



 


GGCAACCAAAGTGGGTGCACTGTCTAAAGGTCAGTTGAAAGAGTTCCTCGACGCTAACCTGG



 


CCGGTTCTGGTTCTGGCCATATGGCTAGCCATCACCACCACCACCACAGCAGCGGCATTGAC



 


GGCCGGCATAGCGATGGCATCTTTACCGATAGCTATAGCCGCTATCGCAAACAGATGGCGGT



 


GAAAAAGTATCTGGCGGCGGTGCTGGGCTAATAA-3′







The sequence of SEQ ID NO: 55 is a sequence derived from pET32aPACAP (a pET32 derivative) that has been prepared by inserting both an NdeI fragment comprising pET32a-derived thioredoxin gene and an artificial gene of PACAP into the NheI site of pET21b.
In sequences (IX) to (XIV), N2 is a nucleotide sequence complementary to the nucleotide sequence of N1. As a specific example of N2, the following sequence may be given.









3′-GTGGACTGACTGCTGTCAAAACTGTGCCTACATGAGTTTCGCCTGCCCCGCTAGGAGCA
(SEQ ID NO: 56)



 


GCTAAAGACCCGTCTCACCACGCCAGGCACGTTTTACTAGCGGGGCTAAGACCTACTTTAGC



 


GACTGCTTATAGTCCCGTTTGACTGGCAACGTTTTGACTTGTAGCTAGTTTTGGGACCGTGA



 


CGCGGCTTTATACCGTAGGCACCATAGGGCTGAGACGACGACAAGTTTTTGCCACTTCACCG



 


CCGTTGGTTTCACCCACGTGACACATTTCCAGTCAACTTTCTCAAGGAGCTGCGATTGGACC



 


GGCCAAGACCAAGACCGGTATACCGATCGGTAGTGGTGGTGGTGGTGTCGTCGCCGTAACTG



 


CCGGCCGTATCGCTACCGTAGAAATGGCTATCGATATCGGCGATAGCGTTTGTCTACCGCCA



 


CTTTTTCATAGACCGCCGCCACGACCCGATTATT-5′







The sequence of SEQ ID NO: 56 is complementary to the sequence of SEQ ID NO: 55.
The vector of the first invention of the present patent application may comprise the coding region of a specific protein [e.g., glutathione-S-transferase (GST) from mammal, Schistosoma japonicum or Escherichia coli, thioredoxin (TRX), His-His-His-His-His-His (SEQ ID NO:62) (His6), lanthanide binding tag (LBT), Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys (SEQ ID NO:63) (FLAG (registered trademark)), enhanced green fluorescense protein (EGFP), or the like] and express a protein and/or a protein domain encoded by a foreign gene in the form of a fusion protein linked to the specific protein encoded by the above-mentioned coding region when the foreign gene encoding the protein and/or the protein domain is integrated thereinto. In this case, it is convenient that the vector has the two restriction recognition sequences different in nucleotide sequence which are recognized by the first recognition enzyme on the carboxyl terminal side of the coding region of the specific protein, wherein one of the two restriction recognition sequences located proximal to the coding region of the specific protein comprises a part of a restriction recognition sequence recognized by a second restriction enzyme that is different from the first restriction enzyme, but the restriction recognition sequence located distal to the coding region of the specific protein does not comprise the part of the restriction recognition sequence recognized by the second restriction enzyme.
The second invention of the present patent application provides an open circular vector comprising a double-stranded DNA obtainable by treating the closed circular vector of the first invention of the present patent application with the first restriction enzyme.
As a specific example of the open circular vector of the present invention, an open circular vector comprising a double-stranded DNA represented by the following sequences (XV) and (XVI) may be given.









(SEQ ID NO: 15)










5′-X7aX8aGTC-N3-GACX1aX2aT-3′
(XV)


 









(SEQ ID NO: 16)










3′-TX7bX8bCAG-N4-CTGX1bX2b-5′
(XVI)






(in sequences (XV) and (XVI), G is guanine, A is adenine, C is cytosine, and T is thymine;

X7a, X8a, X7b and X8b are each independently any base selected from guanine, adenine, cytosine or thymine; X7a and X7b are bases capable of forming a base pair with each other, X8a and X8b are bases capable of forming a base pair with each other;

X1a, X2a, X1b and X2b are each independently any base selected from guanine, adenine, cytosine or thymine; X1a and X1b are bases capable of forming a base pair with each other, X2a and X2b are bases capable of forming a base pair with each other;

sequence CX1aX2aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV or an isoschizomer thereof;

sequence CX8bX7bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV or an isoschizomer thereof that is included in sequence CX1aX2aT;

5′- and 3′-represent the individual termini of the double-stranded DNA;

N3 is any nucleotide sequence having 2000-7000 bases; and

N4 is a nucleotide sequence complementary to the nucleotide sequence of N3.)

In sequences (XV) and (XVI), preferably, X7a is A, X8a is T, X1a is C, X2a is A, X7b is T, X8b is A, X1b is G, and X2b is T.
As another example of the open circular vector of the present invention, an open circular vector comprising a double-stranded DNA represented by the following sequences (XVII) and (XVIII) may be given.









(SEQ ID NO: 17)



5′-Y13aY14aY15aY16aTGG-N3-CCAY1aY2aY3aY4aT-3′



(XVII)


 



(SEQ ID NO: 18)



3′-TY13bY14bY15bY16bACC-N4-GGTY1bY2bY3bY4b-5′



(XVIII)






(in sequences (XVII) and (XVIII), G is guanine, A is adenine, C is cytosine, and T is thymine;

Y1a, Y2a, Y3a, Y4a, Y1b, Y2b, Y3b and Y4b are each independently any base selected from guanine, adenine, cytosine or thymine; Y1a and Y1b are bases capable of forming a base pair with each other, Y2a and Y2b are bases capable of forming a base pair with each other, Y3a and Y3b are bases capable of forming a base pair with each other, Y4a and Y4b are bases capable of forming a base pair with each other; sequence Y1aY2aY3aY4aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV, AflIII, BspLU11I, NspI, SphI, BspHI, BsaAI, PmaCI, SnaBI, NspBII, PvuII, BanII, HgiAI, SacI or isoschizomer thereof;

Y13a, Y14a, Y15a, Y16a, Y13b, Y14b, Y15b and Y16b are each independently any base selected from guanine, adenine, cytosine or thymine; Y13a and Y13b are bases capable of forming a base pair with each other, Y14a and Y14b are bases capable of forming a base pair with each other, Y15a and Y15b are bases capable of forming a base pair with each other, Y16a and Y16b are bases capable of forming a base pair with each other; sequence Y16bY15bY14bY13bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV, AflIII, BspLU11I, NspI, SphI, BspHI, BsaAI, PmaCI, SnaBI, NspBII, PVuII, BanII, HgiAI, SacI or an isoschizomer that is included in sequence Y1aY2aY3aY4aT;

5′- and 3′-represent the individual termini of the double-stranded DNA;

N3 is any nucleotide sequence having 2000-7000 bases; and

N4 is a nucleotide sequence complementary to the nucleotide sequence of N3.)

In sequences (XVII) and (XVIII), preferably, Y2a is C, Y3a is C, Y4a is A, Y2b is G, Y3b is G, Y4b is T, Y13a is T, Y14a is G, Y15a is T, Y13b is A, Y14b is C, and Y15b is A.
As still another example of the open circular vector of the present invention, an open circular vector comprising a double-stranded DNA represented by the following sequences (XIX) and (XX) may be given.







(SEQ ID NO: 19)








5′-Y13aY14aY15aY16aTGG-N3-GACX1aX2aT-3′
(XIX)


 







(SEQ ID NO: 20)








3′-TY13bY14bY15bY16bACC-5′ N4-CTGX1bX2b-5′
(XX)






(in sequences (XIX) and (XX), G is guanine, A is adenine, C is cytosine, and T is thymine;

Y13a, Y14a, Y15a, Y16a, Y13b, Y14b, Y15b and Y16b are each independently any base selected from guanine, adenine, cytosine or thymine; Y13a and Y13b are bases capable of forming a base pair with each other, Y14a and Y14b are bases capable of forming a base pair with each other, Y15a and Y15b are bases capable of forming a base pair with each other, Y16a and Y16b are bases capable of forming a base pair with each other; X1a, X2a, X1b and X2b are each independently any base selected from guanine, adenine, cytosine or thymine; X1a and X1b are bases capable of forming a base pair with each other, X2a and X2b are bases capable of forming a base pair with each other;

sequence CX1aX2aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV or an isoschizomer thereof;

sequence Y14bY13bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV or an isoschizomer thereof that is included in sequence CX1aX2aT; 5′- and 3′-represent the individual termini of the double-stranded DNA;

N3 is any nucleotide sequence having 2000-7000 bases; and

N4 is a nucleotide sequence complementary to the nucleotide sequence of N3.)

In sequences (XIX) and (XX), preferably, X1a is C, X2a is A, X1b is G, X2b is T, Y13a is T, Y14a is G, Y15a is T, Y13b is A, Y14b is C, and Y15b is A.
In sequences (XV) to (XX), N3 may be, for example, a sequence derived from a commercial vector (e.g., pGEX-4T3, pGEX-2T, pGEX-3X, pET21b, pET32a or the like). As a specific example of N3, the following sequence may be given.









5′-GGATCCCCGAATTCCCGGGTCGACTCGAGCGGCCGCATCGTGACTGACTGACGATCTGC
(SEQ ID NO: 57)



 


CTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCAC



 


AGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTG



 


GCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGGAGTGTATAATTCTTGA



 


AGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTC



 


TTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCT



 


AAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATAT



 


TGAAAAAGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCCGC



 


ATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATC



 


AGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGT



 


TTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGT



 


ATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCCGTCGCCGCATACACTATTCTCAGAATG



 


ACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAA



 


TTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGAT



 


CGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTG



 


ATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCT



 


GCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCG



 


GCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCC



 


TTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATC



 


ATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACCACGGGGAG



 


CCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGC



 


ATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTT



 


TAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACG



 


TGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATC



 


CTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCCGTGGTT



 


TGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCA



 


GATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAG



 


CACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAG



 


TCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTG



 


AACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACC



 


TACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCG



 


GTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTA



 


TCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGT



 


CAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTT



 


TGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTAT



 


TACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAG



 


TGAGCGAGGAAGCGGAAGAGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATT



 


TCACACCGCATAAATTCCGACACCATCGAATGGTGCAAAACCTTTCGCGGTATGGCATGATA



 


GCGCCCGGAAGAGAGTCAATTCAGCGTGGTGAATGTGAAACCAGTAACGTTATACGATGTCG



 


CAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTT



 


TCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCG



 


CGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGG



 


CCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCC



 


AGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAA



 


TCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCA



 


TTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACA



 


CCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGT



 


CGCATTGGGTCACCAGCAAATCCCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTC



 


TGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGG



 


GAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCAT



 


CGTTCCCACTCCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTA



 


CCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGCTAGTGGGATACGACGATACCGAAGAC



 


AGCTCATGTTATATCCCGCCGTTAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAAC



 


CAGCGTCGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGC



 


CCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGC



 


GCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAACCGGGCAGTG



 


AGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGCCACCCCAGGCTTTACACTTTATG



 


CTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTA



 


TGACCATGATTACGGATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGC



 


GTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGA



 


GGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCT



 


GGTTTCCGGCACCAGAAGCGGTGCCCGAAAGCTGGCTGCAGTGCGATCTTCCTGAGGCCGAT



 


ACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGT



 


AACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACT



 


CGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGAT



 


GGCGTTGGAATTACGTTATCGACTGCACGGTGCACCAATGCTTCTGGCGTCAGGCAGCCATC



 


GGAAGCTGTGGTATGGCTGTGCAGGTCGTAAATCACTGCATAATTCGTGTCGCTCAAGGCGC



 


ACTCCCGTTCTGGATAATGTTTTTTGCGCCGACATCATAACGGTTCTGGCAAATATTCTGAA



 


ATGAGCTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGGATAACAAT



 


TTCACACAGGAAACAGTATTCATGTCCCCTATACTAGGTTATTGGAAAATTAAGGGCCTTGT



 


GCAACCCACTCGACTTCTTTTGGAATATCTTGAAGAAAAATATGAAGAGCATTTGTATGAGC



 


GCGATGAAGGTGATAAATGGCGAAACAAAAAGTTTGAATTGGGTTTGGAGTTTCCCAATCTT



 


CCTTATTATATTGATGGTGATGTTAAATTAACACACTCTATGGCCATCATACGTTATATAGC



 


TGACAAGCACAACATGTTGGGTGGTTGTCCAAAAGAGCGTGCAGAGATTTCAATGCTTGAAG



 


GAGCGGTTTTGCATATTAGATACGGTGTTTCGAGAATTGCATATAGTAAAGACTTTGAAACT



 


CTCAAAGTTGATTTTCTTAGCAAGCTACCTGAAATGCTGAAAATGTTCGAAGATCGTTTATG



 


TCATAAAACATATTTAAATGGTGATCATGTAACCCATCCTGACTTCATGTTGTATGACGCTC



 


TTGATGTTGTTTTATACATGGACCCAATGTGCCTGGATGCGTTCCCAAAATTAGTTTGTTTT



 


AAAAAACGTATTGAAGCTATCCCACAAATTGATAAGTACTTGAAATCCAGCAAGTATATAGC



 


ATGGCCTTTGCAGGGCTGGCAAGCCACGTTTGGTGGTGGCGACCATCCTCCAAAATCGGATC



 


TGGTTCCGCGTGCATCC-3′







The sequence of SEQ ID NO: 57 is derived from pGEX-4T3.
In sequences (XV) to (XX), N4 is a nucleotide sequence complementary to the nucleotide sequence of N3. As a specific example of N4, the following sequence may be given.









3′-CCTAGGGGCTTAAGGGCCCAGCTGAGCTCGCCGGCGTAGCACTGACTGACTGCTAGACG
(SEQ ID NO: 58)



 


GAGCGCGCAAAGCCACTACTGCCACTTTTGGAGACTGTGTACGTCGAGGGCCTCTGCCAGTG



 


TCGAACAGACATTCGCCTACGGCCCTCGTCTGTTCGGGCAGTCCCGCGCAGTCGCCCACAAC



 


CGCCCACAGCCCCGCGTCGGTACTGGGTCAGTGCATCGCTATCGCCTCACATATTAAGAACT



 


TCTGCTTTCCCGGAGCACTATGCGGATAAAAATATCCAATTACAGTACTATTATTACCAAAG



 


AATCTGCAGTCCACCGTGAAAAGCCCCTTTACACGCGCCTTGGGGATAAACAAATAAAAAGA



 


TTTATGTAAGTTTATACATAGGCGAGTACTCTGTTATTGGGACTATTTACGAAGTTATTATA



 


ACTTTTTCCTTCTCATACTCATAAGTTGTAAAGGCACAGCGGGAATAAGGGAAAAAACGCCG



 


TAAAACGGAAGGACAAAAACGAGTGGGTCTTTGCGACCACTTTCATTTTCTACGACTTCTAG



 


TCAACCCACGTGCTCACCCAATGTAGCTTGACCTAGAGTTGTCGCCATTCTAGGAACTCTCA



 


AAAGCGGGGCTTCTTGCAAAAGGTTACTACTCGTGAAAATTTCAAGACGATACACCGCGCCA



 


TAATAGGGCACAACTGCGGCCCGTTCTCGTTGAGCCAGCGGCGTATGTGATAAGAGTCTTAC



 


TGAACCAACTCATGAGTGGTCAGTGTCTTTTCGTAGAATGCCTACCGTACTGTCATTCTCTT



 


AATACGTCACGACGGTATTGGTACTCACTATTGTGACGCCGGTTGAATGAAGACTGTTGCTA



 


GCCTCCTGGCTTCCTCGATTGGCGAAAAAACGTGTTGTACCCCCTAGTACATTGAGCGGAAC



 


TAGCAACCCTTGGCCTCGACTTACTTCGGTATGGTTTGCTGCTCGCACTGTGGTGCTACGGA



 


CGTCGTTACCGTTGTTGCAACGCGTTTGATAATTGACCGCTTGATGAATGAGATCGAAGGGC



 


CGTTGTTAATTATCTGACCTACCTCCGCCTATTTCAACGTCCTGGTGAAGACGCGAGCCGGG



 


AAGGCCGACCGACCAAATAACGACTATTTAGACCTCGGCCACTCGCACCCAGAGCGCCATAG



 


TAACGTCGTGACCCCGGTCTACCATTCGGGAGGGCATAGCATCAATAGATGTGGTGCCCCTC



 


GGTCCGTTGATACCTACTTGCTTTATCTGTCTAGCGACTCTATCCACGGAGTGACTAATTCG



 


TAACCATTGACAGTCTGGTTCAAATGAGTATATATGAAATCTAACTAAATTTTGAAGTAAAA



 


ATTAAATTTTCCTAGATCCACTTCTAGCAAAAACTATTAGAGTACTGGTTTTAGGGAATTGC



 


ACTCAAAAGCAAGGTGACTCGCAGTCTGGGGCATCTTTTCTAGTTTCCTAGAAGAACTCTAG



 


GAAAAAAAGACGCGCATTAGACGACGAACGTTTGTTTTTTTCGTGGCGATGGTCGCCACCAA



 


ACAAACGGCCTAGTTCTCGATGGTTGAGAAAAAGGCTTCCATTGACCGAAGTCGTCTCGCGT



 


CTATGGTTTATGACAGGAAGATCACATCGGCATCAATCCGGTGGTGAAGTTCTTGAGACATC



 


GTGGCGGATGTATGGAGCGAGACGATTAGGACAATGGTCACCGACGACGGTCACCGCTATTC



 


AGCACAGAATGGCCCAACCTGAGTTCTGCTATCAATGGCCTATTCCGCGTCGCCAGCCCGAC



 


TTGCCCCCCAAGCACGTGTGTCGGGTCGAACCTCGCTTGCTGGATGTGGCTTGACTCTATGG



 


ATGTCGCACTCGATACTCTTTCGCGGTGCGAAGGGCTTCCCTCTTTCCGCCTGTCCATAGGC



 


CATTCGCCGTCCCAGCCTTGTCCTCTCGCGTGCTCCCTCGAAGGTCCCCCTTTGCGGACCAT



 


AGAAATATCAGGACAGCCCAAAGCGGTGGACACTGAACTCGCAGCTAAAAACACTACGAGCA



 


GTCCCCCCGCCTCGGATACCTTTTTGCGCTCGTTGCGCCGGAAAAATGCCAAGGACCGGAAA



 


ACGACCGGAAAACGAGTGTACAAGAAAGGACGCAATAGGGGACTAAGACACCTATTGGCATA



 


ATGGCGGAAACTCACTCGACTATGGCGAGCGGCGTCGGCTTGCTGGCTCGCCTCGCTCAGTC



 


ACTCGCTCCTTCGCCTTCTCGCGGACTACGCCATAAAAGAGGAATGCGTAGACACGCCATAA



 


AGTGTGGCGTATTTAAGGCTGTGGTAGCTTACCACGTTTTGGAAAGCGCCATACCGTACTAT



 


CGCGGGCCTTCTCTCAGTTAAGTCCCACCACTTACACTTTGGTCATTGCAATATGCTACAGC



 


GTCTCATACGGCCACAGAGAATAGTCTGGCAAAGGGCGCACCACTTGGTCCGGTCGGTGCAA



 


AGACGCTTTTGCGCCCTTTTTCACCTTCGCCGCTACCGCCTCGACTTAATGTAAGGGTTGGC



 


GCACCGTGTTGTTGACCGCCCGTTTGTCAGCAACGACTAACCGCAACGGTGGAGGTCAGACC



 


GGGACGTGCGCGGCAGCGTTTAACAGCGCCGCTAATTTAGAGCGCGGCTAGTTGACCCACGG



 


TCGCACCACCACAGCTACCATCTTGCTTCGCCGCAGCTTCGGACATTTCGCCGCCACGTGTT



 


AGAAGAGCGCGTTGCGCAGTCACCCGACTAGTAATTGATAGGCGACCTACTGGTCCTACGGT



 


AACGACACCTTCGACGGACGTGATTACAAGGCCGCAATAAAGAACTACAGAGACTGGTCTGT



 


GGGTAGTTGTCATAATAAAAGAGGGTACTTCTGCCATGCGCTGACCCGCACCTCGTAGACCA



 


GCGTAACCCAGTGGTCGTTTAGCGCGACAATCGCCCGGGTAATTCAAGACAGAGCCGCGCAG



 


ACGCAGACCGACCGACCGTATTTATAGAGTGAGCGTTAGTTTAAGTCGGCTATCGCCTTGCC



 


CTTCCGCTGACCTCACGGTACAGGCCAAAAGTTGTTTGGTACGTTTACGACTTACTCCCGTA



 


GCAAGGGTGACGCTACGACCAACGGTTGCTAGTCTACCGCGACCCGCGTTACGCGCGGTAAT



 


GGCTCAGGCCCGACGCGCAACCACGCCTATAGAGCCATCACCCTATGCTGCTATGGCTTCTG



 


TCGAGTACAATATAGGGCGGCAATTGGTGGTAGTTTGTCCTAAAAGCGGACGACCCCGTTTG



 


GTCGCACCTGGCGAACGACGTTGAGAGAGTCCCGGTCCGCCACTTCCCGTTAGTCGACAACG



 


GGCAGAGTGACCACTTTTCTTTTTGGTGGGACCGCGGGTTATGCGTTTGGCGGAGAGGGGCG



 


CGCAACCGGCTAAGTAATTACGTCGACCGTGCTGTCCAAAGGGCTGACCTTTCGCCCGTCAC



 


TCGCGTTGCGTTAATTACACTCAATCGAGTGAGTAATCCGTGGGGTCCGAAATGTGAAATAC



 


GAAGGCCGAGCATACAACACACCTTAACACTCGCCTATTGTTAAAGTGTGTCCTTTGTCGAT



 


ACTGGTACTAATGCCTAAGTGACCGGCAGCAAAATGTTGCAGCACTGACCCTTTTGGGACCG



 


CAATGGGTTGAATTAGCCGAACGTCCTGTAGGGGGAAAGCGGTCGACCGCATTATCGCTTCT



 


CCGGGCGTGGCTAGCGGGAAGGGTTGTCAACGCGTCGGACTTACCGCTTACCGCGAAACGGA



 


CCAAAGGCCGTGGTCTTCGCCACGGCCTTTCGACCGACCTCACGCTAGAAGGACTCCGGCTA



 


TGACAGCAGCAGGGGAGTTTGACCGTCTACGTGCQAATGCTACGCGGGTACATGTGGTTGCA



 


TTGGATAGGGTAATGCCAGTTAGGCGGCAAACAAGGGTGCCTCTTAGGCTGCCCAACAATGA



 


GCGAGTGTAAATTACAACTACTTTCGACCGATGTCCTTCCGGTCTGCGCTTAATAAAAACTA



 


CCGCAACCTTAATGCAATAGCTGACGTGCCACGTGGTTACGAAGACCGCAGTCCGTCGGTAG



 


CCTTCGACACCATACCGACACGTCCAGCATTTACTGACGTATTAAGCACAGCGAGTTCCGCG



 


TGAGGGCAAGACCTATTACAAAAAACGCGGCTGTAGTATTGCCAAGACCGTTTATAAGACTT



 


TACTCGACAACTGTTAATTAGTAGCCGAGCATATTACACACCTTAACACTCGCCTATTGTTA



 


AAGTGTGTCCTTTGTCATAAGTACAGGGGATATGATCCAATAACCTTTTAATTCCCGGAACA



 


CGTTGGGTGAGCTGAAGAAAACCTTATAGAACTTCTTTTTATACTTCTCGTAAACATACTCG



 


CGCTACTTCCACTATTTACCGCTTTGTTTTTCAAACTTAACCCAAACCTCAAAGGGTTAGAA



 


GGAATAATATAACTACCACTACAATTTAATTGTGTCAGATACCGGTAGTATGCAATATATCG



 


ACTGTTCGTGTTGTACAACCCACCAACAGGTTTTCTCGCACGTCTCTAAAGTTACGAACTTC



 


CTCGCCAAAACCTATAATCTATGCCACAAAGCTCTTAACGTATATCATTTCTGAAACTTTGA



 


GAGTTTCAACTAAAAGAATCGTTCGATGGACTTTACGACTTTTACAAGCTTCTAGCAAATAC



 


AGTATTTTGTATAAATTTACCACTAGTACATTGGGTAGGACTGAAGTACAACATACTGCGAG



 


AACTACAACAAAATATGTACCTGGGTTACACGGACCTACGCAAGGGTTTTAATCAAAGAAAA



 


TTTTTTGCATAACTTCGATAGGGTGTTTAACTATTCATGAACTTTAGGTCGTTCATATATCG



 


TACCGGAAACGTCCCCACCGTTCGGTdCAAACCACCACCGCTGGTAGGAGGTTTTAGCCTAG



 


ACCAAGGCGCACCTAGG-5′







The sequence of SEQ ID NO: 58 is complementary to the sequence of SEQ ID NO: 57.
The third invention of the present patent application provides a recombinant vector in which a foreign gene is integrated into the vector of the first invention of the present patent application, the foreign gene comprising a sequence designed in such a manner that a restriction recognition sequence for the second restriction enzyme does not occur when the foreign gene is inserted in the proper orientation into the vector of the first invention treated with the first restriction enzyme, but the restriction recognition sequence for the second restriction enzyme occurs when the foreign gene is inserted thereinto in the opposite orientation. A recombinant vector in which a foreign gene is inserted in the proper direction into the vector of the first invention of the present patent application treated with the first restriction enzyme is preferable. The foreign gene may encode a protein and/or a protein domain.
The fourth invention of the present patent application provides a transformant comprising the recombinant vector of the third invention of the present patent application, or a progeny thereof.
The fifth invention of the present patent application provides a method of preparing the vector of the first invention of the present patent application, comprising introducing into a multicloning site of a plasmid, phage, cosmid, P1 vector, bacterial artificial chromosome vector or yeast artificial chromosome vector a double-stranded DNA comprising two restriction recognition sequences different in nucleotide sequence which are recognized by a first restriction enzyme, one of the restriction recognition sequences comprising a part of a restriction recognition sequence recognized by a second restriction enzyme that is different from the first restriction enzyme, and the other one of the restriction recognition sequences not comprising the part of the restriction recognition sequence recognized by the second restriction enzyme.
The sixth invention of the present patent application provides a double-stranded DNA comprising two restriction recognition sequences different in nucleotide sequence which are recognized by a first restriction enzyme, one of the restriction recognition sequences comprising a part of a restriction recognition sequence recognized by a second restriction enzyme that is different from the first restriction enzyme, and the other one of the restriction recognition sequences not comprising the part of the restriction recognition sequence recognized by the second restriction enzyme.
As a specific example of the double-stranded DNA of the sixth invention of the present patent application, a double-stranded DNA represented by the following sequences (IX) and (X) may be given.







(SEQ ID NO: 9)


5′-GACX1aX2aTX3aX4aGTC-N1-GACX5aX6aAX7aX8aGTC-3′


(IX)


 


(SEQ ID NO: 10)


3′-CTGX1bX2bAX3bX4bCAG-N2-CTGX5bX6bTX7bX8bCAG-5′


(X)






(in sequences (IX) and (X), G is guanine, A is adenine, C is cytosine, and T is thymine;

X1a to X8a and X1b to X8b are each independently any base selected from guanine, adenine, cytosine or thymine; X1a and X1b are bases capable of forming a base pair with each other, X2a and X2b are bases capable of forming a base pair with each other, X3a and X3b are bases capable of forming a base pair with each other, X4a and X4b are bases capable of forming a base pair with each other, X5a and X5b are bases capable of forming a base pair with each other, X6a and X6b are bases capable of forming a base pair with each other, X7a and X7b are bases capable of forming a base pair with each other, X8a and X8b are bases capable of forming a base pair with each other;

sequence CX1aX2aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV or an isoschizomer thereof;

sequence CX8bX7bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV or an isoschizomer thereof that is included in sequence CX1aX2aT;

5′- and 3′-represent the individual termini of the double-stranded DNA;

N1 may not exist, and when it exists it is any nucleotide sequence having 1-1000 bases; and

N2 may not exist, and when it exists it is a nucleotide sequence complementary to the nucleotide sequence of N1.)

As another specific example of the double-stranded DNA of the sixth invention of the present patent application, a double-stranded DNA represented by the following sequences (XI) and (XII) may be given.







(SEQ ID NO: 11)








5′-CCAY1aY2aY3aY4aTY5aY6aY7aY8aTGG-N1-
(XI)


CCAY9aY10aY11aY12aAY13aY14aY15aY16aTGG-3′



 







(SEQ ID NO: 12)








3′-GGTY1bY2bY3bY4bAY5bY6bY7bY8bACC-N2-
(XII)


GGTY9bY10bY11bY12bTY13bY14bY15bY16bACC-5′







(in sequences (XI) and (XII), G is guanine, A is adenine, C is cytosine, and T is thymine;

Y1a to Y16a and Y1b to Y16b are each independently any base selected from guanine, adenine, cytosine or thymine; Y1a and Y1b are bases capable of forming a base pair with each other, Y2a and Y2b are bases capable of forming a base pair with each other, Y3a and Y3b are bases capable of forming a base pair with each other, Y4a and Y4b are bases capable of forming a base pair with each other, Y5a and Y5b are bases capable of forming a base pair with each other, Y6a and Y6b are bases capable of forming a base pair with each other, Y7a and Y7b are bases capable of forming a base pair with each other, Y8a and Y8b are bases capable of forming a base pair with each other, Y9a and Y9b are bases capable of forming a base pair with each other, Y10a and Y10b are bases capable of forming a base pair with each other, Y11a and Y11b are bases capable of forming a base pair with each other, Y12a and Y12b are bases capable of forming a base pair with each other, Y13a and Y13b are bases capable of forming a base pair with each other, Y14a and Y14b are bases capable of forming a base pair with each other, Y15a and Y15b are bases capable of forming a base pair with each other, Y16a and Y16b are bases capable of forming a base pair with each other sequence Y1aY2aY3aY4aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV, AflIII, BspLU11I, NspI, SphI, BspHI, BsaAI, PmaCI, SnaBI, NspBII, PvuII, BanII, HgiAI, SacI or an isoschizomer thereof;

sequence Y16bY15bY14bY13bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV, AflIII, BspLU11I, NspI, SphI, BspHI, BsaAI, PmaCI, SnaBI, NspBII, PvuII, BanII, HgiAI, SacI or an isoschizomer thereof that is included in sequence Y1aY2aY3aY4aT;

5- and 3-represent the individual termini of the double-stranded DNA;

N1 may not exist, and when it exists it is any nucleotide sequence having 1-1000 bases; and

N2 may not exist, and when it exists it is a nucleotide sequence complementary to the nucleotide sequence of N1.)

As a still another example of the double-stranded DNA of the sixth invention of the present patent application, a double-stranded DNA represented by the following sequences (XIII) and (XIV) may be given.







(SEQ ID NO: 13)








5′-GACX1aX2aTX3aX4aGTC-N1-
(XIII)


CCAY9aY10aY11aY12aAY13aY14aY15aY16aTGG-3′



 







(SEQ ID NO: 14)








3′-CTGX1bX2bAX3bX4bCAG-N2-
(XIV)


GGTY9bY10bY11bY12bTY13bY14bY15bY16bACC-5′







(in sequences (XIII) and (XIV), G is guanine, A is adenine, C is cytosine, and T is thymine;

X1a to X4a and X1b to X4b are each independently any base selected from guanine, adenine, cytosine or thymine; X1a and X1b are bases capable of forming a base pair with each other, X2a and X2b are bases capable of forming a base pair with each other, X3a and X3b are bases capable of forming a base pair with each other, X4a and X4b are bases capable of forming a base pair with each other;

Y9a to Y16a and Y9b to Y16b are each independently any base selected from guanine, adenine, cytosine or thymine; Y9a and Y9b are bases capable of forming a base pair with each other, Y10a and Y10b are bases capable of forming a base pair with each other, Y11a and Y11b are bases capable of forming a base pair with each other, Y12a and Y12b are bases capable of forming a base pair with each other, Y13a and Y13b are bases capable of forming a base pair with each other, Y14a and Y14b are bases capable of forming a base pair with each other, Y15a and Y15b are bases capable of forming a base pair with each other, Y16a and Y16b are bases capable of forming a base pair with each other, sequence CX1aX2aT is a nucleotide sequence comprising a partial sequence on 5′ side of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI, SspI, EcoRV or an isoschizomer thereof;

sequence Y14bY13bT is a nucleotide sequence not comprising the partial sequence of the restriction recognition sequence of NcoI, DsaI, EcoT14I, NdeI, SfeI, AvaI, SmlI, XhoI, PstI, EcoT22I, PshBI, AccI, ApaLI, PsiI, ScaI, SplI, Bsp1107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlhI, NheI, XbaI, SspI, EcoRV or an isoschizomer thereof that is included in sequence CX1aX2aT;

5′- and 3′-represent the individual termini of the double-stranded DNA;

N1 may not exist, and when it exists it is any nucleotide sequence having 1-1000 bases; and

N2 may not exist, and when it exists it is a nucleotide sequence complementary to the nucleotide sequence of N1.)

The seventh invention of the present patent application provides a method of producing a protein and/or a protein domain encoded by a foreign gene, using the vector of the first invention of the present patent application.
In one embodiment of the seventh invention, a recombinant vector may be prepared by integrating into the first vector of the present application a foreign gene which encodes a protein and/or a protein domain and comprises a sequence designed in such a manner that a restriction recognition sequence for the second restriction enzyme does not occur when the foreign gene is inserted in the proper orientation into the vector of the first invention treated with the first restriction enzyme, but the restriction recognition sequence for the second restriction enzyme occurs when the foreign gene is inserted thereinto in the opposite orientation. This recombinant vector may be treated with the second restriction enzyme and then introduced into a host to thereby allow the host to form single colonies. By culturing the single colony-derived host, it is possible to express the protein and/or the protein domain encoded by the foreign gene.
In another embodiment of the seventh invention of the present application, a primer may be used which comprises a sequence designed in such a manner that a restriction recognition sequence for the second restriction enzyme does not occur when the foreign gene is inserted in the proper orientation into the vector of the first invention treated with the first restriction enzyme, but the restriction recognition sequence for the second restriction enzyme occurs when the foreign gene is inserted thereinto in the opposite orientation and which is capable of amplifying the cDNA of a foreign gene encoding a protein and/or protein domain. Using the cDNA as a template, DNA mixtures corresponding to cDNA partial sequences different in location and/or length and/or a part of the sequence of the cDNA may be amplified. Each of the thus amplified mixtures is integrated into the vector of the first invention treated with the first restriction enzyme to thereby prepare a recombinant vector. The recombinant vector is treated with the second restriction enzyme and then introduced into a host to thereby allow the host to form single colonies. By culturing the single colony-derived host, it is possible to express the protein and/or the protein domain encoded by the foreign gene.
The eighth invention of the present patent application provides a method of linearizing a recombinant vector in which a foreign gene is inserted in the opposite orientation and allowing a recombinant vector in which the foreign gene is inserted in the proper orientation to remain unlinearized, using the vector of the first invention of the present patent application.
In one embodiment of the eighth invention of the present patent application, the recombinant vector of the third invention of the present patent application may be treated with the second restriction enzyme to thereby linearize the vector in which a foreign gene is inserted in the opposite orientation and allowing the vector in which the foreign gene is inserted in the proper orientation to remain unlinearized.
The ninth invention of the present patent application provides a method of testing the expression level and/or the solubility of a protein and/or protein domain encoded by a foreign gene, using the vector of the first invention of the present patent application.
In one embodiment of the ninth invention of the present patent application, a recombinant vector may be prepared by integrating into the first vector of the present application a foreign gene which encodes a protein and/or a protein domain and comprises a sequence designed in such a manner that a restriction recognition sequence for the second restriction enzyme does not occur when the foreign gene is inserted in the proper orientation into the vector of the first invention treated with the first restriction enzyme, but the restriction recognition sequence for the second restriction enzyme occurs when the foreign gene is inserted thereinto in the opposite orientation. This recombinant vector may be treated with the second restriction enzyme and then introduced into a host. By culturing the host and/or its progeny, it is possible to express the protein and/or the protein domain encoded by the foreign gene and to examine the expression level and/or the solubility of the thus expressed protein and/or protein domain.
Sequence (I) is shown in SEQ ID NO: 1 of the sequence listing.
Sequence (II) is shown in SEQ ID NO: 2 of the sequence listing.
Sequence (III) is shown in SEQ ID NO: 3 of the sequence listing.
Sequence (IV) is shown in SEQ ID NO: 4 of the sequence listing.
Sequence (V) is shown in SEQ ID NO: 5 of the sequence listing.
Sequence (VI) is shown in SEQ ID NO: 6 of the sequence listing.
Sequence (VII) is shown in SEQ ID NO: 7 of the sequence listing.
Sequence (VIII) is shown in SEQ ID NO: 8 of the sequence listing.
One example of sequence (IX) (when N1 has one base) is shown in SEQ ID NO: 9 of the sequence listing.
One example of sequence (X) (when N2 has one base) is shown in SEQ ID NO: 10 of the sequence listing.
One example of sequence (XI) (when N1 has one base) is shown in SEQ ID NO: 11 of the sequence listing.
One example of sequence (XII) (when N2 has one base) is shown in SEQ ID NO: 12 of the sequence listing.
One example of sequence (XIII) (when N3 has one base) is shown in SEQ ID NO: 13 of the sequence listing.
One example of sequence (XIV) (when N4 has one base) is shown in SEQ ID NO: 14 of the sequence listing.
One example of sequence (XV) (when N3 has one base) is shown in SEQ ID NO: 15 of the sequence listing.
One example of sequence (XVI) (when N4 has one base) is shown in SEQ ID NO: 16 of the sequence listing.
One example of sequence (XVII) (when N3 has one base) is shown in SEQ ID NO: 17 of the sequence listing.
One example of sequence (XVIII) (when N4 has one base) is shown in SEQ ID NO: 18 of the sequence listing.
One example of sequence (XIX) (when N3 has one base) is shown in SEQ ID NO: 19 of the sequence listing.
One example of sequence (XX) (when N4 has one base) is shown in SEQ ID NO: 20 of the sequence listing.
In the present specification, the term “protein domain” refers to a partial sequence of a protein and means a polypeptide having any one of the following properties by itself: some physiological activity, biochemical function, characteristic physicochemical property or tertiary structure.
The expression “(a foreign gene) is inserted in the proper orientation” means that the ORF contained in the gene is inserted into a plasmid in the proper orientation relative to the direction of translation of the plasmid.
The expression “(a foreign gene) is inserted in the opposite orientation” means that the ORF contained in the gene is inserted into a plasmid in the opposite orientation relative to the direction of translation of the plasmid.
The term “restriction recognition sequence” refers to the nucleotide sequence of a double-stranded DNA inherent to each restriction enzyme, which is recognized and cut by the restriction enzyme.
The term “restriction enzyme site” refers to the restriction recognition sequence of a specific restriction enzyme.
The term “multicloning site” refers to a nucleotide sequence in a vector which is designed so that a plurality of restriction enzyme sites occur consecutively.
The term “transformant” refers to a cell which has acquired a novel character as a result of introduction of a foreign gene (DNA), wherein the character is inherited to progeny cells.
The term “host” refers to a living cell into which a recombinant DNA molecule is introduced in recombinant DNA experiments.
The term “vector” refers to a DNA which delivers a heterogenous DNA to a host in recombinant DNA experiments.
The expression “single-colony derived host (or transformant)” refers to a host (or transformant) which has been obtained by inoculating living cells into a medium after sufficient dilution, culturing the cells until they form colonies, separating single colonies, and further culturing those single colonies.
Effect of the Invention
According to the present invention, a vector is provided which is capable of allowing expression of a protein and/or a protein domain by simple operations and in a short period of time.
Further, according to the present invention, a method of allowing expression of proteins and/or protein domains by simple operations and in a short period of time is provided.
Further, according to the present invention, a method of testing the expression level and the solubility of a protein and/or a protein domain by simple operations and in a short period of time is provided.
The present specification encompasses the contents disclosed in the specification and/or drawings of Japanese Patent Application No. 2003-308773 upon which the present patent application claims priority.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows construction of dGST-T vector (pGEX-4T3-PRESAT) (SEQ ID NOS 132 & 64-66 respectively in order of appearance).
FIG. 2 shows the principle of the selection of ORF orientation. FIG. 2 shows an example where the second restriction enzyme is NcoI, and rear PCR primer is so designed to have 5′-GG. When an insert amplified with this primer is inserted into the plasmid in the opposite orientation, an NcoI site appears at the TA-cloning site. When the second restriction enzyme is NdeI, the rear PCR primer may be designed to have 5′-ATG instead of 5′-GG (SEQ ID NOS 67-70 are disclosed respectively in order of appearance).
FIG. 3 is a scheme of a high-throughput method of determining the domain boundary of soluble protein domains using a dGST-T vector. (i) Various PCR primers are designed and used to amplify a series of partial cDNA fragments of interest which are presumed to contain a protein domain. (ii) These fragments are inserted into pGEX-4T3-PRESAT, which is then selected for ORF orientation with NcoI or NdeI and transformed into E. coli for colony isolation. (iii) Individual colonies are cultured in 96-well plates to allow expression of the protein of interest and/or protein domain of interest with varied lengths as GST-fusion proteins. (iv) The quantities of the fusion proteins are determined by CDNB color development assay. Those clones expressing high levels of GST-fusion protein are selected for further analysis.
FIG. 4 shows the results of analysis of GST-fusion protein expression with 15% SDS-PAGE. Lane M represents molecular weight standards; lanes a1-a5 represent yeast Vps4; lanes b1-b5 represent human Vps4; lanes c1-c5 represent mouse Vps4; lanes d1-d5 represent human Snx15a; and lanes e1-e5 represent mouse Snx15a.
FIG. 5 shows the results of analysis of the solubility of GST-fusion proteins immediately after cell disruption, with 15% SDS-PAGE. Lane M represents molecular weight standards; lanes i1-s1 represent yeast Vps4; lanes i2-s2 represent human Vps4; lanes i3-s3 represent mouse Vps4; lanes i4-s4 represent human Snx15a; and lanes i5-s5 represent mouse Snx15a. Lanes marked with “i” are insoluble fractions and lanes marked with “s” are soluble fractions.
FIG. 6 shows the results of measurement of the solubility of GST-fusion proteins immediately after cell disruption by an assay using 1-chloro-2,4-dinitrobenzene (a method for measuring GST enzyme activity). In this Figure, the horizontal axis shows the time (unit: min) after the start of the reaction and the vertical axis shows UV absorbance at 350 nm. In this graph, Δ represents yeast Vps4; ∘ represents human Vps4b; ● represents mouse Vps4b; □ represents human Snx15a; and ▴ represents mouse Snx15a.
FIG. 7 is a scheme of a high-throughput solubility test for protein domains using a dGST-T vector. Approximate time required for each of the indicated operations is given in [ ]. (i) Specific PCR primers are designed and used to amplify a partial cDNA fragment of interest. This partial cDNA fragment may be any partial sequence presumed to contain the entire protein or the protein domain of interest. (ii) This fragment is inserted into pGEX-4T3-PRESAT followed by ligation. (iii) The resultant plasmid is transformed into E. coli DH5a. (iv) Liquid culture is conducted. (v) The plasmid is isolated and purified. (vi) The plasmid is digested with NcoI or NdeI for ORF selection. (vii) The selected plasmid is transformed into E. coli BL21 to (viii) allow formation of E. coli colonies. (ix) IPTG solution is sprayed thereto for inducing protein expression. (x) E. coli cells on agar medium are suspended and collected. (xi) Cells are disrupted to obtain total cell lysate, soluble fraction and insoluble fraction. (xii) SDS-PAGE is conducted to judge the quantity of GST-fusion protein contained in the soluble fraction based on the thickness of the band on the stained gel. The total time required for the entire process from (i) to (xii) is approximately 48 hours.
FIG. 8 shows the results of solubility test. Briefly, cDNA fragments encoding the domains of mVps4b and mSNX15a, respectively, are integrated into pGST-4T3-PRESTAT by TA-cloning. After ORF selection with NcoI, colonies formed on agar medium were subjected to expression induction on agar medium without allowing formation of single colonies. Lane M represents molecular weight standards; lanes t1, s1 and i1 represent GST-mouse Vps4b fusion protein samples without expression induction; lanes t2, s2 and i2 represent GST-mouse Vps4b fusion protein samples with expression induction using IPTG spray; lanes t3, s3 and i3 represent GST-mouse SNX15a fusion protein samples without expression induction; lanes t4, s4 and i4 represent GST-mouse SNX15a fusion protein samples with expression induction using IPTG spray; and “t”, “i” and “s” represent total cell, insoluble fraction and soluble fraction, respectively. The arrow marks indicate bands of fusion proteins of which expression was confirmed. Mark Δ indicates the band which was believed to be GST alone.



BEST MODE FOR CARRYING OUT THE INVENTION
Hereinbelow, preferred embodiments of the present invention will be described in detail.
1. Preparation of Vectors
First, a vector is provided. For example, a commercial vector may be purchased and, when this vector has restriction recognition sequences recognized by a first and second restriction enzymes, mutations may be introduced into these restriction recognition sequences. When this vector is a fusion protein expression vector, it is convenient for the following reasons: it is easy to detect/measure the expression level/solubility of the protein and/or protein domain of interest; it is easy to purify the protein and/or protein domain of interest; and such a vector is advantageous in conducting biochemical experiments for functional analysis/interaction analysis of the protein of interest. In Example 1 described later, mutation was introduced into pGEX-4T3 vector using a 5′ phosphorylated DNA represented by SEQ ID NO: 21 by site-directed mutagenesis. As a result of this mutagenesis, the AhdI site which pGEX-4T3 originally had in its sequence becomes uncleavable.
Subsequently, a linker is provided which is used for introducing into the above vector two restriction recognition sequences which are different in nucleotide sequence but are both recognized by the first restriction enzyme (only one of these restriction sequences comprises a part of the restriction recognition sequence of the second restriction enzyme that is different from the first restriction enzyme). This linker is designed so that it has a restriction enzyme site at both ends for introduction into the multicloning site of the vector and has the two restriction recognition sequences which are different in nucleotide sequence but are both recognized by the first restriction enzyme (only one of these restriction sequences comprises a part of the restriction recognition sequence of the second restriction enzyme that is different from the first restriction enzyme). In Example 1 described later, PCR was performed using pET32aPACAP (a derivative from pET32a vector) as a template and a pair of primers represented by the sequences of SEQ ID NOS: 22 and 24. As a result, a PCR product with BamHI sites at both ends was obtained; to each of the BamHI sites, AhdI site was linked. This PCR product was subcloned into a TA-cloning vector pGEM-T. After confirmation of the sequence, the plasmid was prepared/purified and then digested with restriction enzyme BamHI to thereby obtain an approx. 500 bp fragment (AhdI linker).
The above-described vector (mutation-introduced pGEX-4T3 vector in Example 1 described later) is linearized with a restriction enzyme (BamHI in Example 1 described later), dephosphorylated, ligated to the above-described linker (AhdI linker in Example 1 described later) and transformed into E. coli. Subsequently, plasmids are prepared/purified from transformants derived from a plurality of single colonies. Their nucleotide sequences are confirmed to select those plasmids in which the linker was introduced in the proper orientation. The thus selected plasmids are treated with the first restriction enzyme (AhdI in Example 1 described later) to thereby obtain an open circular vector (pGEX-4T3-PRESAT in Example 1 described later).
2. Preparation of Foreign Genes
A foreign gene is prepared. This foreign gene comprises a sequence which is designed in such a manner that the restriction recognition sequence of the second restriction enzyme does not appear when this gene is inserted into the vector prepared in 1 above in the proper orientation, but the restriction recognition sequence of the second restriction enzyme occurs when this gene is inserted in the opposite orientation. The foreign gene may encode a protein and/or a protein domain.
The foreign gene may be prepared, for example, by PCR. As a template, a cDNA, plasmid, synthetic DNA, RNA or the like comprising a gene of interest may be used. As primers, two oligonucleotides which are complementary to the DNA sequences at both terminals of the gene of interest may be used. These primers must be designed exactly in advance so that the following conditions are satisfied: for one of these primers, the reading frame of translation should not shift after insertion into the vector and, for the other one of these primers, a sequence of 1-10 bases not included in the gene of interest should be added at its 5′ end.
The PCR reaction is usually performed by repeating 20 to 40 cycles, one cycle consisting of the three reactions of dissociation of two DNA strands, annealing with oligonucleotides, and synthesis of complementary strands by DNA polymerase. By using an enzyme having DNA reverse transcription activity in the first reaction, it is also possible to amplify DNA from RNA.
The nucleotide sequences of the primers are designed in such a manner that the restriction recognition sequence of the second restriction enzyme does not occur when the PCR product is inserted into the vector prepared in 1 above in the proper orientation, but the restriction recognition sequence of the second restriction enzyme occurs when the PCR product is inserted in the opposite orientation. In Example 2 described later, the front primer (primer corresponding to the N-terminal of the ORF of the cDNA) was designed in such a manner that (i) it starts with the first codon of any amino acid so that the reading frame coincides with that of the preceding GST and (ii) the 5′-end nucleotides of this primer do not start with 5′-GG. The rear primer (primer corresponding to the C-terminal of the ORF) was designed in such a manner that (i) a stop codon is contained after the boundary of the presumed C terminal region of the protein domain and (ii) the 5′-end nucleotides of this primer start with 5′-GG. As a result, the PCR product amplified with these primers has an NcoI site generated only when it has been ligated to pGEX-4T3-PRESAT in the opposite orientation. This newly generated NcoI site is used in the subsequent selection step.
Other matters to be attended to in designing PCR primers for amplifying DNA to be integrated into pGEX-4T3-PRESAT for recombinant protein production will be described below.
(1) When the First Restriction Enzyme is AhdI and the Second Restriction Enzyme is NcoI (NcoI Selection)
The primer corresponding to the N-terminal of the ORF may be designed according to the following four rules.
(ia) The first base of the primer sequence must correspond to the first base of an amino acid codon so that the reading frame coincides with the reading frame of the preceding GST.
(iia) The base at 5′-end must be G or A. (If necessary, a DNA sequence encoding a small number of amino acids may be inserted.)
(iiia) 5′-end sequence must not be GG.
(iva) NcoI restriction enzyme site must not be included in the PCR amplified fragment.
The primer corresponding to the C-terminal of the ORF may be designed according to the following two rules.
(va) 5′-end sequence must be GG.
(via) When the protein domain of interest does not contain a stop codon, 5′-end sequence must start with GG-Xn-TTA [where Xn may be any bases in a number of n (where n is an integer from 0 to 30); e.g., Xn may be A] (an example of sequence where n=5 is shown in SEQ ID NO: 53).

(2) When the First Restriction Enzyme is AhdI and the Second Restriction Enzyme is NdeI (NdeI Selection)

The primer corresponding to the N-terminal of the ORF may be designed according to the following four rules.
(ib) The first base of the primer sequence must correspond to the first base of an amino acid codon so that the reading frame coincides with the reading frame of the preceding GST.
(iib) The base at 5′-end must be G or A. (If necessary, a DNA sequence encoding a small number of amino acids may be inserted.)
(iiib) 5′-end sequence must not be ATG.
(ivb) NdeI restriction enzyme site must not be included in the PCR amplified fragment.
The primer corresponding to the C-terminal of the ORF may be designed according to the following two rules.
(vb) 5′-end sequence must be ATG.
(vib) When the protein domain of interest does not contain a stop codon, 5′-end sequence must start with ATG-Xn-TTA [where Xn may be any bases in a number of n (where n is an integer from 0 to 30); e.g., Xn may be A] (an example of sequence where n=4 is shown in SEQ ID NO: 54).

3. Cloning

The foreign gene prepared in 2 above is ligated to the vector prepared in 1 above (pGEX-4T3-PRESAT vector in Example 2 described later), which is then transformed into E. Coli. The transformed E. coli is not inoculated into agar medium or allowed single colony formation. The transformant is cultured in liquid medium, from which a plasmid mixture is purified. When this plasmid mixture is treated with the second restriction enzyme (NcoI in Example 2 described later), those plasmids in which the foreign gene has been inserted into the vector in the opposite orientation are cut at the newly generated restriction site of the second restriction enzyme and linearized. On the other hand, those plasmids in which the foreign gene has been inserted into the vector in the proper orientation remain unlinearized. Therefore, when the plasmid mixture treated with the second restriction enzyme is transformed into an E. coli host for expression and the resultant transformant is spread on agar medium, only those E. coli cells which harbor a plasmid where the foreign gene has been inserted into the vector in the proper orientation form colonies. From each of the single colonies formed on the agar-medium, E. coli is collected, cultured and allowed to express a fusion protein. Those E. coli cells which have completed expression are harvested and disrupted by sonication or the like to thereby prepare a total cell lysate fraction. Further, the total cell lysate fraction is centrifuged to obtain the supernatant as a soluble fraction. The precipitate is dissolved completely with an SDS-containing buffer of the same volume as that of the solubilized fraction, to thereby prepare an insoluble fraction. The total cell lysate fraction alone or each of the total cell lysate fraction, soluble fraction and insoluble fraction is analyzed by SDS-PAGE, followed by confirmation of the band of the protein of interest on the gel. Subsequently, a ratio between the soluble fraction and the insoluble fraction is determined from the thickness of the bands of the fusion protein on the gel. This ratio is used as an indicator for the solubility of the fusion protein of interest (solubility test). It will be still better to quantitatively determine protein bands on the gel using densitometry or the like.
Solubility tests using the enzyme activity of GST are performed based on the method described in the Amersham Pharmacia's manual for handling pGEX series vectors. Briefly, E. coli soluble fraction containing the fusion protein of interest diluted in an appropriate buffer is placed in a cuvette in a UV spectrophotometer. After 1-chloro-2,4-dinitrobenzene and reduced glutathione are added thereto and agitated thoroughly, time course of UV absorbance at 340 nm is measured consecutively up to 5 to 10 minutes. The resultant slope is used as an indicator for the amount of the fusion protein of interest. When a large number of samples are handled in parallel, use of a microplate reader is convenient.
After the above-described operations, clones which are good in the expression level and solubility of the fusion protein of interest are selected. Then, plasmids are purified and their nucleotide sequences are determined. A plasmid comprising the foreign gene of interest is employed as an expression vector for the protein and/or protein domain, and used in subsequent mass production experiments. According to this method, it has become possible to reduce the time period required for preparing an expression vector for a protein and/or protein domain of interest by about 30% compared to the conventional method.
4. Mass Production of Proteins and/or Protein Domains
The protein and/or protein domain expression vector employed in 3 above is transformed into an E. coli host for expression. The resultant transformant is cultured and allowed to express the protein and/or protein domain of interest. When the protein and/or protein domain expression vector is a fusion protein expression vector, it is convenient for the following reasons: it is easy to detect/measure the expression level/solubility of the protein and/or protein domain of interest (e.g., detection by means of fluorescence, calorimetric assay using the enzyme activity of GST as an indicator, etc.); it is easy to purify the protein and/or protein domain of interest (e.g., one step purification using GSH-immobilized beads is possible); and such a vector is advantageous in conducting biochemical experiments for functional analysis/interaction analysis of the protein of interest (e.g., in vitro binding experiment using BIACORE, in vitro binding experiments using pull down assay, etc.).
Isolation and purification of the expressed protein and/or protein domain may be performed by known methods. Known methods of isolation and purification include, but are not limited to, methods using solubility (such as salting out and solvent precipitation); methods using difference in molecular weight (such as dialysis, ultra-filtration, gel filtration, and SDS-polyacrylamide gel electrophoresis); methods using difference in electric charge (such as ion exchange chromatography); methods using specific affinity (such as affinity chromatography); methods using difference in hydrophobicity (such as reversed phase HPLC and hydrophobic chromatography); and methods using difference in isoelectric point (such as isoelectric focusing).
The present invention has been described so far using E. coli as a host. However, the host used in the present invention is not limited to E. coli. Examples of hosts which may be used in the present invention include, but are not limited to, bacterial cells (e.g., Escherichia bacteria, Bacillus bacteria, Bacillus subtilis), fungal cells (e.g., budding yeast, fission yeast, Aspergillus), insect cells (e.g., S2 cells, Sf cells), animal cells (e.g., CHO cells, COS cells, HeLa cells, C127 cells, 3T3 cells, BHK cells, HEK293 cells) and plant cells.
The first restriction enzyme, second restriction enzyme, two restriction recognition sequences different in nucleotide sequence which are recognized by the first restriction enzyme (one comprising a part of the restriction recognition sequence recognized by the second restriction enzyme, and the other not comprising that part) and pair of PCR primers for preparing a foreign gene used in the present invention are not limited to those described above. The enzymes and sequences summarized in the following Tables (I II and III) may be used. In the Tables, G is guanine, A is adenine, C is cytosine, T is thymine, X is any base, and Xn represents any bases in a number of n (where n is an integer from 0 to 30).
Table I











TABLE I








Restriction recognition
Restriction recognition





sequence (i) of first
sequence (ii) of first





restriction enzyme
restriction enzyme

Restriction



(comprising a part
(not comprising

recognition



(underlined portion) of the
the part the

sequence


First
restriction recognition
restriction recognition
Second
of second


restriction
sequence of second
sequence of second
restriction
restriction


enzyme
restriction enzyme)
restriction enzyme)
enzyme
enzyme





Ahdt
5′-GACCATTGGTC-3′
5′-GACAAAATGTC-3′
NcoI
5′-CCATGG-3′



3′-CTGGTAACCAG-5′
3′-CTGTTTTACAG-5′
DsaI
3′-GGTACC-5′



(SEQ ID NO: 71)
(SEQ ID NO: 77)
EcoT14I



 



5′-GACCATTGGTC-3′
5′-GACAAAATGTC-3′
NdeI
5′-CATATG-3′



3′-CTGGTAACCAG-5′
3′-CTGTTTTACAG-5′

3′-GTATAC-5′



(SEQ ID NO: 71)
(SEQ ID NO: 77)




 



5′-GACXCTTGGTC-3′
5′-GACAAAATGTC-3′
Sfe I
5′-CTATAG-3′



3′-CTGXGAACCAG-5′
3′-CTGTTTTACAG-5′

3′GATATC-5′



(X is any base)
(SEQ ID NO: 77)





(SEQ ID NO: 72)





 



5′-GACTATTGGTC-3′
5′GACAAAATGTC-3′
Sfe I
5′-CTATAG-3′



3′-CTGATAACCAG-5′
3′CTGTTTTACAG-5′

3′-GATATC-5′



(SEQ ID NO: 73)
(SEQ ID NO: 77)




 



5′-CACAATTGGTC-3′
5′GACAAAATGTC-3′
Mun I
5′-CAATTG-3′



3′CTGTTAACCAG-5′
3′-CTGTTTTACAG-5′

3′-GTTAAC-5′



(SEQ ID NO: 74)
(SEQ ID NO: 77)




 



5′-GACGATTGGTC-3′
5′GACAAAATGTC-3′
Mcr I
5′-CGATCG-3′



3′-CTGCTAACCAG-5′
3′-CTGTTTTACAG-5′
Pvu I
3′-GCTAGC-5′



(SEQ ID NO: 75)
(SEQ ID NO: 77)




 



5′-GACXCTTGGTC-3′
5′-GACAAAATGTC-3′
Ava I
5′CTCGAG-3′



3′-CTGXGAACCAG-5′
3′-CTGTTTTACAG-5′
Sml I
3′-GAGCTC-5′



(X is any base)
(SEQ ID NO: 77)
Xho I




(SEQ ID NO: 72)





 



5′-GACXCTTGGTC-3′
5′-GACAAAATGTC-3′
Pst I
5′-CTGCAG-3′



3′-CTGXGAACCAG-5′
3′-CTGTTTTACAG-5′
Sfe I
3′GACGTC-5′



(X is any base)
(SEQ ID NO: 77)





(SEQ ID NO: 72)





 



5′GACXCTTGGTC-3′
5′-GACAAAATGTC-3′
Afl II
5′-CTTAAG-3′



3′-CTGXGAACCAG-5′
3′-CTGTTTTACAG-5′
Sml I
3′-GAATTC-5′



(X is any base)
(SEQ ID NO: 77)





(SEQ ID NO: 72)





 



5′-GACXATTGGTC-3′
5′-GACAAAATGTC-3′
Cla I
5′-ATCGAT-3′



3′-CTGXTAACCAG-5′
3′-CTGTTTTACAG-5′

3′-TAGCTA-5′



(X is any base)
(SEQ ID NO: 77)





(SEQ ID NO: 76)





 



5′-GACXATTGGTC-3′
5′-GACAAAATGTC-3′
EcoT221
5′-ATGCAT-3′



3′-CTGXTAACCAG-5′
3′-CTGTTTTACAG-5′

3′TACGTA-5′



(X is any base)
(SEQ ID NO: 77)





(SEQ ID NO: 76)





 



5′-GACXATTGGTC-3′
5′-GACAAAATGTC-3′
PshB I
5′-ATTAAT-3′



3′-CTGXTAACCAG-5′
3′-CTGTTTTACAG-5′

3′-TAATTA-5′



(X is any base)
(SEQ ID NO: 77)





(SEQ ID NO: 76)





 



5′-GACATTTGGTC-3′
5′-GACAAATTGTC-3′
PshB I
5′-ATTAAT-3′



3′-CTGTAAACCAG-5′
3′-CTGTTTAACAG-5′

3′-TAATTA-5′



(SEQ ID NO: 78)
(SEQ ID NO: 86)




 



5′-GACXGTTGGTC-3′
5′-GACAAAATGTC-3′
Acc I
5′-GTATAC-3′



3′-CTGXCAACCAG-5′
3′-CTGTTTTACAG-5′
Bst1107 I
3′-CATATG-5′



(X is any base)
(SEQ ID NO: 77)





(SEQ ID NO: 79)





 



5′-GACXGTTGGTC-3′
5′-GACAAAATGTC-3′
Acc I
5′-GTCGAC-3′



3′-CTGXCAACCAG-5′
3′-CTGTTTTACAG-5′
Hinc II
3′CAGCTG-5′



(X is any base)
(SEQ ID NO: 77)
Sal I




(SEQ ID NO: 79)





 



5′-GACXGTTGGTC-3′
5′-GACAAAATGTC-3′
ApaL I
5′GTGAC-3′



3′-CTGXCAACCAG-5′
3′-CTGTTTTACAG-5′
Bsp1286 I
3′-CACTG-5



(X is any base)
(SEQ ID NO: 77)
HgiA I




(SEQ ID NO: 79)





 



5′-GACXGTTGGTC-3′
5′-GACAAAATGTC-3′
Hinc II
5′-GTTAC-3′



3′-CTGXCAACCAG-5′
3′-CTGTTTTACAG-5′
Hpa I
3′-CAATTG-5′



(X is any base)
(SEQ ID NO: 77)





(SEQ ID NO: 79)





 



5′GACXTTTGGTC-3′
5′-GACAAATTGTC-3′
Psi I
5′-TTATAA-3′



3′-CTGXAAACCAG-5′
3′-CTGTTTAACAG-5′

3′-AATATT-5′



(X is any base)
(SEQ ID NO: 86)





(SEQ ID NO: 80)





 



5′-GACXTTTGGTC-3′
5′-GACAAATTGTC-3′
NspV
5′-TTCGAA-3′



3′-CTGXAAACCAG-5′
3′-CTGTTTAACAG-5′
BspT1041
3′-AAGCTT-5′



(X is any base)
(SEQ ID NO: 86)





(SEQ ID NO: 80)





 



5′GACXTTTGGTC-3′
5′-GACAAATTGTC-3′
Dra I
5′-TTTAAA-3′



3′-CTGXAAACCAG-5′
3′-CTGTTTAACAG-5′

3′-AAATTT-5



(X is any base)
(SEQ ID NO: 86)





(SEQ ID NO: 80)





 



5′-GACAGTTGGTC-3′
5′GACAAAATGTC-3′
Sca I
5′-AGTACT-3′



3′CTGTCAACCAG-5′
3′-CTGTTTTACAG-5′
Tat I
3′-TCATGA-5′



(SEQ ID NO: 81)
(SEQ ID NO: 77)




 



5′-GACCGTTGGTC-3′
5′-GACAAAATGC-3′
Spl I
5′-CGTACG-3′



3′-CTCGCAACCAG-5′
3′-CTGTTTTACAG-5′

3′-GCATGC-5′



(SEQ ID NO: 82)
(SEQ ID NO: 77)




 



5′GACGGTTGGTC-3′
5′GACAAAATGTC-3′
BspT107I
5′-GGTACC-3′



3′CTGCCAACCAG-5′
3′CTGTTTTACAG-5′
HgiCI
3′-CCATGG-5′



(SEQ ID NO: 83)
(SEQ ID NO: 77)
Kpn I



 



5′GACTGTTGGTC-3′
5′-GACAAAAGTC-3′
Bsp1407 I
5′-TGTACA-3′



3′-CTGACAACCAG-5′
3′-CTGTTTTACAG-5′
Tat I
3′-ACATGT-5′



(SEQ ID NO: 84)
(SEQ ID NO: 77)




 



5′-GACACTTGGTC-3′
5′-GACAAAATGTC-3′
Spe I
5′-ACTAGT-3′



3′-CTGTGAACCAG-5′
3′-CGTTTTACAG-5′

3′-TGATCA-5′



(SEQ ID NO: 85)
(SEQ ID NO: 77)




 



5′-GACCCTTGGTC-3′
5′-GACAAAATGTC-3′
Bln I
5′-CCTAGG-3′



3′-CTGGGAACCAG-5′
3′-CTGTTTTACAG-5′
EcoT14I
3′-GGATCC-5′



(SEQ ID NO: 87)
(SEQ ID NO: 77)




 



5′-GACGCTTGGTC-3′
5′GACAAAATGTC-3′
Nhe I
5′-GCTAGC-3′



3′-CTGCGAACCAG-5′
3′CTGTTTTACAG-5′

3′-CGATCG-5′



(SEQ ID NO: 88)
(SEQ ID NO: 77)




 



5′-GACTCTTGGTC-3′
5′-GACAAAATGTC-3′
Xba I
5′-TCTAGA-3′



3′-CTGAGAACCAG-5′
3′-CTGTTTTACAG-5′

3′-AGATCT-5′



(SEQ ID NO: 89)
(SEQ ID NO: 77)




 



5′-GACAATTGGTC-3′
5′-GACAAAATGTC-3′
Ssp I
5′-AATATT-3′



3′-CTGTTAACCAG-5′
3′-CTGTTTTACAG-5′

3′-TTATAA-5′



(SEQ ID NO: 74)
(SEQ ID NO: 77)




 



5′-GACGATTGGTC-3′
5′-GACAAAATGTC-3′
EcoRV
5′-GATATC-3′



3′-CTGCTAACCAG-5′
3′-CTGTTTTACAG-5′

3′-CTATAG-5′



(SEQ ID NO: 75)
(SEQ ID NO: 77)

















5′-end and 3′-







end sequences

Sequence
Sequence




of a foreign

added
added




gene to be
Requirement
to the 5′
to the 5′




inserted into a
that the 5′-
end of rear
end of rear




vector (large
end sequence
primer for
primer for




letter “A”
of front
preparing a
preparing a




represents the base
primer for
foreign gene
foreign gene



First
of a nucleotide
preparing a
(when stop
(when stop



restriction
added in
foreign gene
codon is
codon is



enzyme
PCR reaction)
must satisfy
not added)
also added)






Ahdt
5′-XXXX-//-XXCA-3′
Not including
5′-GG
5′-GGXnTTA




3′-AXXXX-//-XXGG-5′
5′-GG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCATA-3′
Not including
5′-ATG
5′ATGXnTTA




3′AXXXX-//-XXGTA-5′
5′-ATG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTATA-3′
Not including
5′-ATG
5′ATAGXnTTA




3′-AXXXX-//-XXGATA-5′
5′-ATAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTA-3′
Not including
5′-AG
5′-AGXnTTA




3′-AXXXX-//-XXGA-5′
5′-AG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCA-3′
Not including
5′-TG
5′-TGXnTTA




3′-AXXXX-//-XXGT-5′
5′-TG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCGA-3′
Not including
5′-CG
5′-CGXnTTA




3′-AXXXX-//-XXGC-5′
5′-CG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTCGA-3′
Not including
5′-CGAG
5′CGAGXnTTA




3′-AXXXX-//-XXGAGC-5′
5′-GCAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTGCA-3′
Not including
5′-GCAG
5′GCAGXnTTA




3′-AXXXX-//-XXGAGG-5′
5′-GCAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTTAA-3′
Not including
5′-TAAG
5′-TAAGXnTTA




3′-AXXXX-//-XXGAAT-5′
5′-TAAG 

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXATCGA-3′
Not including
5′-CGAT
5′-CGATXnTTA




3′-AXXXX-//-XXTAGC-5′
5′-CGAT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXATGCA-3′
Not including
5′-GCAT
5′-GCATXnTTA




3′AXXXX-//-XXTACG-5′
5′-GCAT)

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXATTA-3′
Not including
5′-TAAT
5′-TAATXnTTA




3′AXXX-//-XXTAAT-5′
5′-TAAT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXATTA-3′
Not including
5′-AAT
5′-AATXnTTA




3′-AXXX-//-XXTAA-5′
5′-AAT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTATA-3′
Not including
5′-ATAC
5′-ATACXnTTA




3′-AXXXX-//-XXCATA-5′
5′-ATAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTCGA-3′
Not including
5′-CGAC
5′-CGACXnTTA




3′-AXXXX-//-XXCAGC-5′
5′-CGAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTGCA-3′
Not including
5′-GCAC
5′GCACXnTTA




3′-AXXXX-//-XXCACG-5′
5′-GCAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTTAA-3′
Not including
5′-TAAC
5′TAACXnTTA




3′-AXXXX-//-XXCAAT-5′
5′-TAAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTATA-3′
Not including
5′-ATAA
5′-ATAAXnTTA




3′-AXXX-//-XXAATA-5′
5′-ATAA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTCGA-3′
Not induding
5′-CGAA
5′-CGAAXnTTA




3′-AXXXX-//-XXAAGC-5′
5′-CGAA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTTAA-3′
Not including
5′-TAAA
5′-TAAAXnTTA




3′-AXXXX-//-XXAAAT-5′
5′-TAAA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTA-3′
Not including
5′-ACT
5′-ACTXnTTA




3′-AXXXX-//-XXTCA-5′
5′-ACT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGGTA-3′
Not including
5′-ACG
5′-ACGXnTTA




3′-AXXXX-//-XXGCA-5′
5′-ACG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGGTA-3′
Not induding
5′-ACC
5′-ACCXnTTA




3′-AXXXX-//-XXCCA-5′
5′-ACC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTA-3′
Not including
5′-ACA
5′-ACAXnTA




3′-AXXXX-//-XXCA-5′
5′-ACA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXACTA-3′
Not including
5′-AGT
5′-AGTXnTTA




3′-AXXXX//-XXTGA-5′
5′-AGT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCCTA-3′
Not including
5′-AGG
5′-AGGXnTTA




3′-AXXX-//-XXGA-5′
5′-AGG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGCTA-3′
Not including
5′-AGC
5′-AGCXnTTA




3′-AXXXX-//-XXCGA-5′
5′-AGC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTCTA-3′
Not including
5′-AGA
5′-AGAXnTTA




3′-AXXXX-//-XXAGA-5′
5′-AGA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXAATA-3′
Not including
5′-ATT
5′-ATTXnTTA




3′-AXXXX-//-XXTTA-5′
5′-ATT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGATA-3′
Not including
5′-ATC
5′ATCXnTTA




3′-AXXXX-//-XXCTA-5′
5′-ATC

(Xn represents any




(X is any base)


bases in a number







of n)




















TABLE II








Restriction recognition
Restriction recognition





sequence (i) of first
sequence (ii) of first





restriction enzyme
restriction enzyme

Restriction



(comprising a part
(not comprising

recognition



(underlined portion) of the
the part of the

sequence


First
restriction recognition
restriction recognition
Second
of second


restriction
sequence of second
sequence of second
restriction
restriction


enzyme
restriction enzyme)
restriction enzyme)
enzyme
enzyme





Ahdt/XccmI
5′-GACCATTCGTC-3′
5′-CCAATAAATGGCTGG-3′
NcoI
5′-CCATCG-3′



3′-CTGGTAAACCAG-5′
3′-GGTTATTTACCGACC-5′
DsaI
3′-GGTACC-5′



(SEQ ID NO: 71)
(SEQ ID NO: 90)
EcoT14I



 



5′-GACCATTGGTC-3′
5′-CCAATAAATGGCTGG-3′
NdeI
5′-CATATG-3′



3′-CTGGTAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-GTATAC-5′



(SEQ ID NO: 71)
(SEQ ID NO: 90)




 



5′-GACXCTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Sfe I
5′-CTATAG-3′



3′-CTGXGAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-GATATC-5′



(X is any base)
(SEQ ID NO: 90)





(SEQ ID NO: 72)





 



5′-GACTATTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Sfe I
5′-CTATAG-3′



3′-CTGATAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-GATATC-5′



(SEQ ID NO: 73)
(SEQ ID NO: 90)




 



5′-GACAATTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Mun I
5′-CAATTG-3′



3′-CTGTTAACAG-5′
3′-GGTTATTTTACGACC-5′

3′-GTTAAC-5′



(SEQ ID NO: 74)
(SEQ ID NO: 90)




 



5′-GACGATTGGTC-3′
5′-CCAATAAAAGGCTGG-3′
Mcr I
5′-CGATCG-3′



3′-CTGCTAACCAG-5′
3′-GGTTATTTACCGAGC-5′
Pvu I
3′-GCTAGC-5′



(SEQ ID NO: 75)
(SEQ ID NO: 90)




 



5′-GACXCTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Ava I
5′-CTCGAG-3′



3′-CTGXGAACCAG-5′
3′-GGTTATTTACGGACC-5′
Sml I
3′-GAGCTC-5′



(X is any base)
(SEQ ID NO: 90)
Xho I




(SEQ ID NO: 72)





 



5′-GACXCTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Pst I
5′-CTGCAG-3′



3′-CTGXGAACCAG-5′
3′-GGTTATTTACCGACC-5′
Sfe I
3′-GACGTC-5′



(SEQ ID NO: 72)
(SEQ ID NO: 90)




 



5′-GACXCTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
AFl II
5′-CTTAAG-3′



3′-CTCXGAACCAG-5′
3′-GGTTATTTACGGACC-5′
Sml I
3′-GAATTC-5′



(X is any base)
(SEQ ID NO: 90)





(SEQ ID NO: 72)





 



5′-GACXATTGGTC-3′
5′-CCAATAAATGGCTCG-3′
Cla I
5′-ATCGAT-3′



3′-CTGXTAACCAG-5′
3′-GGTTATTTACGGACC-5′

3′-TAGCTA-5′



(X is any base)
(SEQ ID NO: 90)

(X is any base)



(SEQ ID NO: 76)





 



5′-GACXATTGGTC-3′
5′-CCAATAAATCGCTGG-3′
EcoT221
5′-ATGGAT-3′



3′-CTGXTAACCAG-5′
3′-GGTTAATTTACCAGAC-5′

3′-TAGGTA-5′



(X is any base)
(SEQ ID NO: 90)





(SEQ ID NO: 76)





 



5′-GACXATTGGTC-3′
5′-CCAATAAATGGCTGG-3′
PshB I
5′-ATTAAT-3′



3′-GTGXTAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-TAATA-5′



(X is any base)
(SEQ ID NO: 90)





(SEQ ID NO: 76)





 



5′-GACATTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
PshB I
5′-ATTAAT-3′



3′-CTGTAAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-TAATTA-5′



(SEQ ID NO: 78)
(SEQ ID NO: 90)




 



5′-GACXGTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Acc I
5′-GTATAC-3′



3′-CTGXCAACCAG-5′
3′-GGTTATTTACGGACC-5′
Bst1107 I
3′-CATATG-5′



(X is any base)
(SEQ ID NO: 90)





(SEQ ID NO: 79)





 



5′-GACXGTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Acc I
5′-GTCGAC-3′



3′-CTGXCAACCAG-5′
3′-GGTTATTTACCGACC-5′
Hinc II
3′-CAGGTG-5′



(X is any base)
(SEQ ID NO: 90)
Sal I




(SEQ ID NO: 79)





 



5′-GACXGTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
ApaL I
5′-CTGCAG-3′



3′-CTGXCAACCAG-5′
3′-GGTTATTTACCGACC-5′
Bsp1286 I
3′-CACGTG-5′



(X is any base)
(SEQ ID NO: 90)
HgiAI
(X is any base)



(SEQ ID NO: 79)





 



5′-GACXGTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Hinc II
5′-GTTAAC-3′



3′-CTGXCAACCAG-5′
3′-GGTTATTTACCGACC-5′
Hpa I
3′-CAATTG-5′



(X is any base)
(SEQ ID NO: 90)





(SEQ ID NO: 79)





 



5′-GACXTTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Psi I
5′-TTATAA-3′



3′-CTGXAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-AATAAT-5′



(X is any base)
(SEQ ID NO:90)





(SEQ ID NO: 80)





 



5′-GACXTTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Nsp V
5′-TTCGAA-3′



3′-CTGXAAACCAG-5′
3′-GGTTATTTACCGACC-5′
BspT1041
3′-AAGCTT-5′



(X is any base)
(SEQ ID NO: 90)





(SEQ ID NO: 80)





 



5′-CACXTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Dra I
5′-TTTAAA-3′



3′-CTGXAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-AAATTT-5′



(X is any base)
(SEQ ID NO: 90)





(SEQ ID NO: 80)





 



5′-GACAGTTGGTC-3′
5′-CCAATAAAGGCTGG-3′
Sca I
5′-AGTACT-3′



3′-CTGTCAACCAG-5′
3′-GGTTATTTACCGACC-5′
Tat I
3′-TCATGA-5′



(SEQ ID NO: 81)
(SEQ ID NO: 90)




 



5′-GACCGTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Spl I
5′-CGTACG-3′



3′-CTGGCAACCAG-5′
3′-GGTTATTACGACC-5′

3′-GCATGC-5′



(SEQ ID NO: 82)
(SEQ ID NO: 90)




 



5′-GACGGTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
BspT107 I
5′-GGTACC-3′



3′-CTGCCAACCAG-5′
3′-GGTTATTTACCGACC-5′
HgiC I
3′-CCATGG-5′



(SEQ ID NO: 83)
(SEQ ID NO: 90)
Kpn I



 



5′-GACTGTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Bsp1407 I
5′-TGTACA-3′



3′-CTGACAACCAG-5′
3′-GGTTATTTACCGACC-5′
Tat I
3′-ACATGT-5′



(SEQ ID NO: 84)
(SEQ ID NO: 90)




 



5′-GACACTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Spe I
5′-ACTAGT-3′



3′-CTGTGAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-TGATCA-5′



(SEQ ID NO: 85)
(SEQ ID NO: 90)




 



5′-GACCCTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Bln I
5′-CCTAGG-3′



3′-CTGGGAACCAG-5′
3′-GGTTATTTACCGACC-5′
EcoT14I
3′-GGATCC-5′



(SEQ ID NO: 87)
(SEQ ID NO: 90)




 



5′-GACGCTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Nhe I
5′-GCTAGC-3′



3′-CTGCGAACCAG-5′
3′-GGTTATTTAGGAGC-5′

3′-CGATCG-5′



(SEQ ID NO: 88)
(SEQ ID NO: 90)




 



5′-GACTCTTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Xba I
5′-TCTAGA-3′



3′-CTGAGAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-AGATCT-5′



(SEQ ID NO: 89)
(SEQ ID NO: 90)




 



5′-GACAATTGGTC-3′
5′-CCAATAAATGGCTGG-3′
Ssp I
5′-AATATT-3′



3′-CTGTTAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-TTATAA-5′



(SEQ ID NO: 74)
(SEQ ID NO: 90)




 



5′-GACGATTGGTC-3′
5′-CCAATAAATGGCTGG-3′
EcoRV
5′GATATC-3′



3′-CTGCTAACCAG-5′
3′-GGTTATTTACCGACC-5′

3′-CTATAG-5′



(SEQ ID NO: 75)
(SEQ ID NO: 90)

















5′-end and 3′-







end sequences

Sequence
Sequence




of a foreign

added
added




gene to be
Requirement
to the 5′
to the 5′




inserted into a
that the 5′-
end of rear
end of rear




vector (large
end sequence
primer for
primer for




letter “A”
of front
preparing a
preparing a




represents the base
primer for
foreign gene
foreign gene



First
of a nucleotide
preparing a
(when stop
(when stop



restriction
added in
foreign gene
codon is
codon is



enzyme
PCR reaction)
must satisfy
not added)
also added)






Ahdt/XccmI
5′-XXXX-//-XXCCA-3′
Not including
5′-GG
5′-GGXnTTA




3′-AXXX-//-XXGG-5′
5′-CG

(Xn represents any




(X is any base)


basis in a number







of n)


 




5′-XXXX-//-XXCATA-3′
Not including
5′-ATG
5′-ATGXnTTA




3′-XXXX-//-XXGTA-5′
5′-ATG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTATA-3′
Not including
5′-ATAG
5′-ATAGXnTTA




3′-AXXXX-//-XXGATA-5′
5′-ATAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTA-3′
Not including
5′-AG
5′-AGXnTTA




3′-AXXXX-//-XXGA-5′
5′-AG

(xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCAA-3′
Not including
5′-TG
5′-TGXnTTA




3′-AXXX-//-XXGT-5′
5′-TG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGGA-3′
Not including
5′-CG
(5′-CGXnTTA




3′-AXXXX-//-XXGC-5′
5′-CG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTCGA-3′
Not including
5′-CGAG
5′-CGAGXnTTA




3′-AXXXX-//-XXGAGC-5′
5′-CGAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTGCA-3′
Not including
5′-GCAG
5′GCAGXnTTA




3′-AXXX-//-XXGACG-5′
5′-GCAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTTAA-3′
Not including
5′-TAAG
5′-TAAGXnTTA




3′-AXXXX-//-XXGAAT-5′
5′-TAAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




Not including 5′-CGAT
5′-CGAT
5′-CGAT
5′-CGATXnTTA







(Xn represents any







bases in a number







of n)


 




Not including 5′-CGAT
5′-CGAT
5′-CGAT
5′-CGATXnTTA







(Xn represents any







bases in a number







of n)


 




5′-XXXX-//-XXATTA-3′
Not including
5′-TAAT
5′-TAATXnTTA




3′-AXXXX-//-XXTAA-5′
5′-TAAT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXATTA-3′
Not including
5′-AAT
5′-AATXXnTTA




3′-AXXXX-//-XXTAA-5′
5′-AAT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTATA-3′
Not including
5′-ATAC
5′-ATACXnTTA




3′-AXXXX-//-XXCATA-5′
5′-ATAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTCGA-3′
Not including
5′-CGAC
5′-CGACXnTTA




3′-AXXXX-//-XXCAGC-5′
5′-CGAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTGCA-3′
Not including
5′-GCAC
5′-GCACXnTTA




3′-AXXXX-//-XXCACG-5′
5′-GCAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTTAA-3′
Not including
5′-TAAC
5′-TAACXnTTA




3′-AXXXX-//-XXCAAT-5′
5′-TAAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTATA-3′
Not including
5′-ATAA
5′-ATAAXnTTA




3′-AXXXX-//-XXAATA-5′
5′-ATAA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTCGA-3′
Not including
5′-CGAA
5′-CGAAXnTTA




3′-AXXXX-//-XXAAGC-′
5′-CGAA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTAA-3′
Not including
5′-TAAA
5′-TAAXnTTA




3′-AXXX-//-XXAAT-5′
5′-TAAA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXAGTA-3′
Not including
5′-ACT
5′-ACTnTTA




3′-AXXXX-//-XXTCA-5′
5′-ACT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCGTA-3′
Not including
5′-ACG
5′-ACGXnTTA




3′-AXXXX-//-XXGCA-5′
5′-ACG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGGTA-3′
Not including
5′-ACC
5′-ACCXnTTA




3′-AXXXX-//-XXCCA-5′
5′-ACC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTGTA-3′
Not including
5′-ACA
5′-ACAXnTTA




3′-AXXXX-//-XXACA-5′
5′-ACA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXACTA-3′
Not including
5′-AGT
5′-AGTXnTTA




3′-AXXXX-//-XXTGA-5′
5′-AGT

5′-AGTXnTTA




(X is any base)


(Xn represents any







bases in a number







of n)


 




5′-XXXX-//-XXCCTA-3′
Not including
5′-ACG
5′-ACGXnTTA




3′-AXXXX-//-XXGGA-5′
5′-ACG

5′-AGTXnTTA




(X is any base)


(Xn represents any







bases in a number







of n)


 




5′-XXXX-//-XXGCTA-3′
Not including
5′-AGC
5′-ACGXnTTA




3′-AXXXX-//-XXCGA-5′
5′-AGC

5′-AGTXnTTA




(X is any base)


(Xn represents any







bases in a number







of n)


 




5′-XXXX-//-XXTCTA-3′
Not including
5′-AGA
5′-AGAXnTTA




3′-AXXXX-//-XXAGA-5′
5′-AGA

5′-AGTXnTTA




(X is any base)


(Xn represents any







bases in a number







of n)


 




5′-XXXX-//-XXAATA-3′
Not including
5′-ATT
5′-ATTXnTTA




3′-AXXXX-//-XXTTA-5′
5′-ATT

5′-AGTXnTTA







(Xn represents any







bases in a number







of n)


 




5′-XXXX-//-XXGATA-3′
Not including
5′-ATC
5′-ATCXnTTA




3′-AXXXX-//-XXCTA-5′
5′-ATC

5′-AGTXnTTA




(X is any base)


(Xn represents any







bases in a number







of n)




















TABLE III








Restriction recognition
Restriction recognition





sequence (i) of first
sequence (ii) of first





restriction enzyme
restriction enzyme

Restriction



(comprising a part
(not comprising

recognition



(underlined portion) of the
the part of the

sequence


First
restriction recognition
restriction recognition
Second
of second


restriction
sequence of second
sequence of second
restriction
restriction


enzyme
restriction enzyme)
restriction enzyme)
enzyme
enzyme





XcmI
5′-CCAXCCATGGTATGG-3′
5′-CCAATAAACCGCTGG-3′
NcoI
5′-CCATGG-3′



3′-GGTXGGTACCATACC-5′
3′-GGTTATTTGCCGACC-5′
DsaI
3′-GGTACC-5′



(SEQ ID NO: 91)
(SEQ ID NO: 98)
EcoT14I



 



5′-CCAXXCATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
NdeI
5′-CATATG-3′



3′-GGTXXGTAACCTACC-5′
3′-GGTTATTTGCCGACC-5′

3′-GTATAC-5



(SEQ ID NO: 92)
(SEQ ID NO: 98)




 



5′-CCAXXXCTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Sfe I
5′-CTATAG-3′



3′-GGTXXXGACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-GATATC-5′



(SEQ ID NO: 93)
(SEQ ID NO: 99)




 



5′-CCAXCTATGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Sfe I
5′-CTATAG-3′



3′-GGTXGACACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-GATATC-5′



(SEQ ID NO: 94)
(SEQ ID NO: 99)




 



5′-CCAXCAATGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Mun I
5′-CAATTG-3′



3′-GGTXGTTACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-GTTAAC-5′



(SEQ ID NO: 95)
(SEQ ID NO: 99)




 



5′-CCAXCGATGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Mcr I
5′-CGATCG-3′



3′-GGTXGCTACCATACC-5′
3′-GGTTATTTACCGACC-5′
Pvu I
3′-GCTAGC-5′



(SEQ ID NO: 96)
(SEQ ID NO: 99)




 



5′-CCAXXXCTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Ava I
5′-CTCGAG-3′



3′-GGTXXXGACCATACC-5′
3′-GGTTATTTACCGACC-5′
Sml I
3′-GAGCTC-5′



(SEQ ID NO: 97)
(SEQ ID NO: 99)
Xho I



 



5′-CCAXXXCTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Pst I
5′-CTGCAG-3′



3′-GGTXXXGACCATACC-5′
3′-GGTTATTTACCGACC-5′
Sfe I
3′-GACGTC-5′



(SEQ ID NO: 97)
(SEQ ID NO: 99)




 



5′-CCAXXXCTGGTATGG-3
5′-CCAATAAATGGCTGG-3′
Afl II
5′-CTTAAG-3′



3′-GGTXXXGACCATACC-5′
3′-GGTTATTTACCGACC-5′
Sml I
3′-GAATTC-5′



(SEQ ID NO: 97)
(SEQ ID NO: 99)




 



5′-CCAXXXATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Cla I
5′-ATCGAT-3′



3′-GGTXXXTACCATACC-5′
3′-GGTATTTGCCGACC-5′

3′-TAGCTA-5′



(SEQ ID NO: 100)
(SEQ ID NO: 105)




 



5′-CCAXXXATGGTATGG-3′
5′-CAATAAACCGCCTGG-3′
EcoT221
5′-ATGCAT-3′



3′-GGTXXXTACCATACC-5′
3′-GGTTATTTGCCGACC-5′

3′-TACGTA-5′



(SEQ ID NO: 100)
(SEQ ID NO: 105)




 



5′-CCAXXXATGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
PshB I
5′-ATTAAT-3′



3′-GGTXXTAACCATACC-5′
3′-GGTTATTTGCCGACC-5′

3′-TAATTA-5′



(SEQ ID NO: 100)
(SEQ ID NO: 105)




 



5′-CCAXXATTGGTATGG-3′
5′-CCAATAAATGCCTGG-3′
PshB I
5′-ATTAAT-3′



3′-GGTXXTAACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-TAATTA-5′



(SEQ ID NO: 101)
(SEQ ID NO: 99)




 



5′-CCAXXXGTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Acc I
5′-GTATAC-3′



3′-GGTXXXCACCATACC-5′
3′-GGTTATTTACCGACC-5′
Bst11071
3′-CATATG-5′



(SEQ ID NO: 102)
(SEQ ID NO: 99)




 



5′-CCAXXXGTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Acc I
5′-GTCGAC-3′



3′-GGXXXCACCATACC-5′
3′-GGTTATTTACCGACC-5′
Hinc II
3′-CAGCTG-5′



(SEQ ID NO: 102)
(SEQ ID NO: 99)
Sal I



 



5′-CCAXXXGTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
ApaL I
5′-GTGCAC-3′



3′-GGTXXXCACCATACC-5′
3′-GGTTATTTACCGACC-5′
Bsp1286 I
3′-CACGTG-5′



(SEQ ID NO: 102)
(SEQ ID NO: 99)
HgiA I



 



5′-CCAXXXGTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Hinc II
5′-GTTAAC-3′



3′-GGTXXXCACCATACC-5′
3′-GGTTATTTACCGACC-5′
Hpa I
3′-CATTG-5′



(SEQ ID NO: 102)
(SEQ ID NO: 99)




 



5′-CCAXXXTTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Psi I
5′-TTATAA-3′



3′-GGTXXXAACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-AATATT-5′



(SEQ ID NO: 103)
(SEQ ID NO: 99)




 



5′-CCAXXXTTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Nsp V
5′-TTCGAA-3′



3′-GGTXXXAACCATACC-5′
3′-GGTTATTTACCGACC-5′
BspT104I
3′-AAGCTT-5′



(SEQ ID NO: 103)
(SEQ ID NO: 99)




 



5′-CCAXXXTTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Dra I
5′-TTTAA-3′



3′-GGTXXXAACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-AAATTT-5′



(SEQ ID NO: 103)
(SEQ ID NO: 99)




 



5′-CCAXXAGTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Sca I
5′-AGTACT-3′



3′-GGTXXTCACCATACC-5′
3′-GGTTATTTACCGACC-5′
Tat I
3′-TCATGA-5′



(SEQ ID NO: 104)
(SEQ ID NO: 99)




 



5′-CCAXXCGTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Spl I
5′-CGTACG-3′



3′-GGTXXGCACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-GCATGC-5′



+B87
(SEQ ID NO: 99)





(SEQ ID NO: 106)





 



5′-CCAXXGGTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
BspT1071
5′-GGTACC-3′



3′-GGTXXCCACCATACC-5′
3′-GGTTATTTACCGACC-5′
HgiC1
3′-CCATGG-5′



(SEQ ID NO: 107)
(SEQ ID NO: 99)
Kpn I



 



5′-CCAXXTGTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Bsp1407 I
5′-TGTACA-3′



3′-GGTXXACACCATACC-5′
3′-GGTTATTTACCGACC-5′
Tat I
3′-ACATGT-5′



(SEQ ID NO: 108)
(SEQ ID NO: 99)




 



5′-CCAXXACTGGTATGG-3′
5′-CCAATAAATGCCTGG-3′
Spe I
5′-ACTAGT-3′



3′-GGTXXTGACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-TGATCA-5′



(SEQ ID NO: 109)
(SEQ ID NO: 99)




 



5′-CCAXXCCTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Bln I
5′-CCTAGG-3′



3′-GGTXXGGACCATACC-5′
3′-GGTTATTTACCGACC-5′
EcoT141
3′-GATCC-5′



(SEQ ID NO: 110)
(SEQ ID NO: 99)




 



5′-CCAXXGCTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Nhe I
5′-GCTAGC-3′



3′-GGTXXCCACCATAAC-5′
3′-GGTTATTTACCGACC-5′

3′-CGATCG-5′



(SEQ ID NO: 111)
(SEQ ID NO: 99)




 



5′-CCAXXTCTGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Xba I
5′-TCTAGA-3′



3′-GGTXXAGACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-AGATCT-5′



(SEQ ID NO: 112)
(SEQ ID NO: 99)




 



5′-CCAXXAATGGTATGG-3′
5′-CCAATAAATGGCTGG-3′
Ssp I
5′-AATATT-3′



3′-GGTXXTTACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-TTATAA-5′



(SEQ ID NO: 113)
(SEQ ID NO: 99)




 



5′-CCAXXGATGGTATGG-3′
3′-CCAATAAATGGCTGG-3′
EcoRV
5′-GATATC-3′



3′-GGTXXCTACCATACC-5′
3′-GGTTATTTACCGACC-5′

3′-CTATAG-5′



(SEQ ID NO: 114)
(SEQ ID NO: 99)




 



5′-CCXAAATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Apo I
5′-AAATTT-3′



3′-GGTXTTTACCATACC-5′
3′-GGTTATTTGCCGACC-5′

3′-TTTAAA-5′



(SEQ ID NO: 115)
(SEQ ID NO: 105)




 



5′-CCAXGAATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Apo I
5′-GAATTC-3′



3′-GGTXCTTACCATACC-5′
3′-GGTTATTTGCCGACC-5′
EcoR I
3′-CTTAAG-5′



(SEQ ID NO: 116)
(SEQ ID NO: 105)




 



5′-CCAXACATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Afl III
5′-ACATGT-3′



3′-GGTXTGTACCATACC-5′
3′-GGTTATTTGCCGACC-5′
BspLU11 I
3′-TGTACA-5′



(SEQ ID NO: 117)
(SEQ ID NO: 105)
Nsp I



 



5′-CCAXGCATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Nsp I
5′-GCATGC-3′



3′-GGTXCGTACCATACC-5′
3′-GGTTATTTGCCGACC-5′
Sph I
3′-CGTACG-5′



(SEQ ID NO: 118)
(SEQ ID NO: 105)




 



5′-CCAXTCATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
BspH I
5′-TCATGA-3′



3′-GGTXAGTACCATACC-5′
3′-GGTTATTTGCCGACC-5′

3′-AGTACT-5′



(SEQ ID NO: 119)
(SEQ ID NO: 105)




 



5′-CCAXAGATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Bgl II
5′-AGATCT-3′



3′-GGTXTCTACCATACC-5′
(SEQ ID NO: 105)
Mfl I
3′-AGTACT-5′



(SEQ ID NO: 120)





 



5′-CCAXGGATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
BamH I
5′-GGATCC-3′



3′-CGTXCCTACCATACC-5′
3′-GGTTATTTGCCGACC-5′
Mfl I
3′-CCTAGG-5′



(SEQ ID NO: 121)
(SEQ ID NO: 105)




 



5′-CCAXTGATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Fba I
5′-TGATCA-3′



3′-GGTXACTACCATACC-5′
3′-GGTTATTTGCCGACC-5′

3′-ACTAGT-5′



(SEQ ID NO: 122)
(SEQ ID NO: 105)




 



5′-CCAXGTATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Acc I
5′-GTATAC-3′



3′-GGTXCATACCATACC-5′
3′-GGTTATTTGCCGACC-5′
Bst1107 I
3′-CATATG-5′



(SEQ ID NO: 123)
(SEQ ID NO: 105)




 



5′-CCAXTTATGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Psi I
5′-TTATAA-3′



3′-GGTXAATACCATACC-5′
3′-GGTTATTTGCCGACC-5′

3′-AATATT-5′



(SEQ ID NO: 124)
(SEQ ID NO: 105)




 



5′-CCAAACGTGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Psp1406 I
5′-AACGTT-3′



3′-GGTTTGCACCATACC-5′
3′-GGTTATTTGCCGACC-5′

3′-TTGCAA-5′



(SEQ ID NO: 125)
(SEQ ID NO: 105)




 



5′-CCACACGTGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
BsaA I
5′-CACGTG-3′



3′-GGTGTGCACCATACC-5′
3′-GGTTATTTGCCGACC-5′
PmaC I
3′-GTGCAC-5′



(SEQ ID NO: 126)
(SEQ ID NO: 105)




 



5′-CCAGACGTGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Aat II
5′-GACGTC-3′



3′-GGTCTGCACCATACC-5′
3′-GGTTATTTGCCGACC-5′
Hin1 I
3′-CTGCAG-5′



(SEQ ID NO: 127)
(SEQ ID NO: 105)




 



5′-CCATACGTGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
BsaA I
5′-TACGTA-3′



3′-GGTTAGCACCATACC-5′
3′-GGTTATTTGCCGACC-5′
SnaB I
3′-ATGCAT-5′



(SEQ ID NO: 128)
(SEQ ID NO: 105)




 



5′-CCAAAGCTGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Hind III
5′-AAGCTT-3′



3′-GGTTTCGACCATACC-5′
3′-GGTTATTTGCCGACC-5′

3′-TTCGAA-5′



(SEQ ID NO: 129)
(SEQ ID NO: 105)




 



5′-CCACACCTGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
NspB II
5′-CAGCTG-3′



3′-GGTGTCGACCATACC-5′
3′-GGTTATTTGCCGACC-5′
Pvu II
3′-GTCGAC-5′



(SEQ ID NO: 130)
(SEQ ID NO: 105)




 



5′-CCAGAGCTGGTATGG-3′
5′-CCAATAAACGGCTGG-3′
Ban II
5′-GAGCTC-3′



3′-GGTCTCGACCATACC-5′
3′-GGTTATTTGCCGACC-5′
Bsp1286 I
3′-CTCGAG-5′



(SEQ ID NO: 131)
(SEQ ID NO: 105)
HgiA I






Sac I

















5′-end and 3′-







end sequences

Sequence
Sequence




of a foreign

added
added




gene to be
Requirement
to the 5′
to the 5′




inserted into a
that the 5′-
end of rear
end of rear




vector (large
end sequence
primer for
primer for




letter “A”
of front
preparing a
preparing a




represents the base
primer for
foreign gene
foreign gene



First
of a nucleotide
preparing a
(when stop
(when stop



restriction
added in
foreign gene
codon is
codon is



enzyme
PCR reaction)
must satisfy
not added)
also added)






XcmI
5′-XXXX-//-XXCCA-3′
Not including
5′-GG
5′-GGXnTA




3′-AXXXX-//-XXGG-5′
5′-GG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCATA-3′
Not including
5′-ATG
5′-ATGXnTTA




3′-AXXXX-//-XXGTA-5′
5′-ATG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTATA-3′
Not including
5′-ATAG
5′-ATAGXnTTA




3′-AXXXX-//-XXGATA-5′
5′-ATAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTA-3′
Not including
5′-AG
5′-AGXnTTA




3′-AXXXX-//-XXGA-5′
5′-AG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCAA-3′
Not including
5′-TG
5′-TGXnTTA




3′-AXXXX-//-XXGT-5′
5′-TG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCGA-3′
Not including
5′-CG
5′-CGXnTTA




3′-AXXXX-//-XXGC-5′
5′-CG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTCGA-3′
Not including
5′-CGAG
5′-CGAGXnTTA




3′-AXXXX-//-XXGAGC-5′
5′-CGAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTGCA-3′
Not including
5′-GCAG
5′-GCAGXnTTA




3′-AXXX-//-XXGACG-5′
5′-GCAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCTTAA-3′
Not including
5′-TAAG
5′-TAAGXnTTA




3′-AXXX-//-XXGAAT-5′
5′-TAAG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXATCGA-3′
Not including
5′-CGAT
5′-CGATXnTTA




3′-AXXX-//-XXTAGC-5′
5′-CGAT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXATGCA-3′
Not including
5′-GCAT
5′-GCATXnTTA




3′-AXXX-//-XXTACG-5′
5′-GCAT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXATTA-3′
Not including
5′-TAAT
5′-TAATXnTTA




3′-AXXX-//-XXTAAT-5′
5′-TAAT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXATTA-3′
Not including
5′-AAT
5′-AATXnTTA




3′-AXXX-//-XXTAA-5′
5′-AAT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTATA-3′
Not including
5′-ATAC
5′-ATACXnTTA




3′-AXXX-//-XXCATA-5′
5′-ATAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTCGA-3′
Not including
5′-GCAC
5′-CGACXnTTA




3′-AXXX-//-XXCAGC-5′
5′-GCAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTGCA-3′
Not including
5′-GCAC
5′-GCACXnTTA




3′-AXXX-/-XXCACG-5′
5′-GCAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTTAA-3′
Not including
5′-TAAC
5′-TAACXnTTA




3′-AXXX-//-XXCATA-5′
5′-TAAC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTATA-3′
Not including
5′-ATAA
5′-ATAAXnTTA




3′-AXXX-//-XXAATA-5′
5′-ATAA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTCGA-3′
Not including
5′-CGAA
5′-CGAAXnTTA




3′-AXXX-//-XXAAGC-5′
5′-CGAA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTAA-3′
Not including
5′-TAAA
5′-TAAAXnTTA




3′-AXXX-//-XXAAAT-5′
5′-TAAA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXAGTA-3′
Not including
5′-ACT
5′-ACTXnTTA




3′-AXXX-//-XXTCA-5′
5′-ACT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCGTA-3′
Not including
5′-ACG
5′-ACGXnTTA




3′-AXXX-//-XXGCA-5′
5′-ACG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGGTA-3′
Not including
5′-ACC
5′-ACCXnTTA




3′-AXXX-//-XXCCA-5′
5′-ACC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTGTA-3′
Not including
5′-ACA
5′-ACAXnTTA




3′-AXXX-//-XXAACA-5′
5′-ACA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXACTA-3′
Not including
5′-AGT
5′-AGTXnTTA




3′-AXXX-//-XXTGA-5′
5′-AGT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXCCTA-3′
Not including
5′-AGG
5′-AGGXnTTA




3′-AXXX-//-XXGGA-5′
5′-AGG

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGCTA-3′
Nothing
5′-AGC
5′-AGCXnTTA




3′-AXXX-//-XXCGA-5′
including

(Xn represents any




(X is any base)
5′-AGC

bases in a number







of n)


 




5′-XXXX-//-XXTCTA-3′
Not including
5′-AGA
5′-AGAXnTTA




3′-AXXXX-//-XXAGA-5′
5′-AGA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXAATA-3′
Not including
5′-ATT
5′-ATTXnTTA




3′-AXXXX-//-XXTTA-5′
5′-ATT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGATA-3′
Not including
5′-ATC
5′-ATCXnTTA




3′-AXXX-//-XXCTA-5′
5′-ATC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXAAA-3′
Not including
5′-TT
5′-TTXnTTA




3′-AXXX-//-XXTT-5
5′-TT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGAA-3′
Not including
5′-TC
5′-TCXnTTA




3′-AXXXX-//-XXCT-5′
5′-TC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXACA-3′
Not including
5′-GT
5′-GTXnTTA




3′-AXXX-//-XXTG-5′
5′-GT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGCA-3′
Not including
5′-GC
5′-GCXnTTA




3′-AXXX-//XXGC-5′
5′-GC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTCA-3′
Not including
5′-GA
5′-GAXnTTA




3′-AXXX-//-XXAG-5′
5′-GA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXAGA-3′
Not including
5′-CT
5′-CTXnTTA




3′-AXXXX-//-XXTC-5′
5′-CT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGGA-3′
Not including
5′-CC
5′-CTXnTTA




3′-AXXXX-//-XXCC-5′
5′-CC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTGA-3′
Not including
5′-CA
5′-CAXnTTA




3′-AXXXX-//-XXAC-5′
5′-CT

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXGTA-3′
Not including
5′-AC
5′-ACXnTTA




3′-AXXXX-//-XXCA-5′
5′-AC

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXTTA-3′
Not including
5′-AA
5′-AAXnTTA




3′-AXXXX-//-XXAA-5′
5′-AA

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXXAA-3′
Not including
5′-T
5′-TXnTTA




3′-AXXXX-//-XXXT-5′
5′-T

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXXCA-3′
Not including
5′-G
5′-GXnTTA




3′-AXXXX-//-XXXG-5′
5′-G

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXXGA-3′
Not including
5′-C
5′-CXnTTA




3′-AXXXX-//-XXXC-5′
5′-C

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXXTA-3′
Not including
5′-A
5′-AXnTTA




3′-AXXXX-//-XXXA-5′
5′-A

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXXAA-3′
Not including
5′-T
5′-TXnTTA




3′-AXXXX-//-XXXT-5′
5′-T

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXXCA-3′
Not including
5′-G
5′-GXnTTA




3′-AXXXX-//-XXXG-5′
5′-G

(Xn represents any




(X is any base)


bases in a number







of n)


 




5′-XXXX-//-XXXGA-3′
Not including
5′-C
5′-CXnTTA




3′-AXXXX-//-XXXC-5′
5′-C

(Xn represents any




(X is any base)


bases in a number







of n)









When the first restriction enzyme is AhdI or an isoschizomer thereof, XcmI or an isoschizomer thereof, or a combination thereof, it is effective to select NcoI, NdeI or an isoschizomer thereof as the second restriction enzyme.
By using the vector of the present invention, it is possible to construct a library which is capable of expressing, as fusion proteins, partial sequences of a protein of interest different in location and/or length in the original protein. For example, a primer mixture is designed and used to amplify partial sequences of a protein of interest using the cDNA of the protein as a template; then, the resultant mixture of DNA fragments encoding partial sequences of the protein are ligated downstream of another protein (for example, see FIG. 3).
Further, by using the vector of the present invention, it becomes possible to create a great number of protein and/or protein domain expression systems in parallel, for example, in 96-well microtiter plates, and to assay the solubility of the proteins and/or protein domains produced by such expression systems in parallel or select only those proteins and/or protein domains with high solubility at high speed (for example, see FIG. 3).
Further, the above-described method using the vector of the present invention and 96-well microtiter plates is capable of creating a great number of protein and/or protein domain expression systems in parallel and also conducting fully automated high-throughput selection of highly soluble proteins and/or protein domains produced, by applying automated colony isolation equipment, automated reagent dispensing/washing equipment capable of handling 96-well microtiter plates or laboratory automation equipment.
Further, by using the vector of the present invention, it becomes possible to judge whether or not a fusion protein comprising a specific single protein and/or protein domain of interest is capable of expression in E. coli, or whether or not the fusion protein is soluble, in 48 hours from the start of PCR reaction at the shortest (for example, see FIG. 7).
EXAMPLES
Hereinbelow, the present invention will be described specifically with reference to the following Examples. It should be noted that these Examples are provided only for the purpose of explanation and do not limit the scope of the present invention.
Restriction enzymes NcoI, NdeI, AhdI and AflII were purchased from New England Biolabs. Restriction enzymes KpnI and BamHI were purchased from Toyobo. T4 DNA ligase, Wizard plasmid miniprepkit and Wizard SV DNA gel purification kit were purchased from Promega. pGEM-T, pGEX-4T3 and pGEX-3X; pET32a; and pET21b were purchased from Promega, Amersham Pharmacia Biotech and Novagen, respectively. pET32aPACAP is a pET32a derivative prepared by inserting pET32a-derived thioredoxin gene-containing NdeI fragment into the NdeI site of pET21b and inserting PACAP artificial gene into the NheI site of the same pET21b. As cDNAs to be used as templates for PCR cloning, QUICK-Clone cDNAs of mouse spleen, mouse embryo and human HeLa cells were purchased from Clontech.
Example 1
Preparation of dGST-T Vector (FIG. 1)
Mutation was introduced into pGEX-4T3 vector using a 5′ phosphorylated DNA represented by the sequence of SEQ ID NO: 21 by site-directed mutagenesis. As a result of this mutagenesis, the AhdI restriction enzyme site which pGEX-4T3 originally had in its sequence becomes uncleavable. Subsequently, PCR reaction was performed using pET32aPACAP vector as a template and a pair of primers represented by the sequences of SED ID NOS: 22 and 24. The resultant PCR product (approx. 500 bp, the sequence of one of the two DNA strands is shown in SEQ ID NO: 25) had an AhdI site linked to each of the two BamHI sites (FIG. 1). This PCR product was subcloned into a TA cloning vector pTEM-T. After confirmation of the sequence, the plasmid was purified. The purified plasmid was digested with restriction enzyme BamHI, followed by purification of an approx. 500 bp fragment (AhdI linker, SEQ ID NOS: 26 and 27). The mutation introduced pGEX-4T3 described above was linearized with BamHI, dephosphorylated and ligated to the above-described AhdI linker. The resultant plasmid was transformed into E. coli. After confirmation of the sequence, those transformants in which AhdI linker was introduced downstream of GST gene in the proper orientation were selected. Approximately 2 μg of the vector into which AhdI linker was introduced downstream of GST gene in the proper orientation was treated with 25 units of AhdI restriction enzyme at 37° C. for 3 hours for digestion, followed by purification using 1% agarose gel. Using Wizard SV gel/PCR clean-up system, an open circular vector of approx. 5 kb (pGEX-4T3-PRERSAT; FIG. 1) was purified and used in the following Examples.
Example 2
Preparation of Novel Expression Systems by Parallel Operation (FIG. 2)
First, using primers appropriate for NcoI selection, five types of genes [regions comprising five MIT domains of SNX15a (human and mouse) and Vps4b (yeast, mouse and human); SEQ ID NOS: 28, 30, 32, 34 and 36] were amplified simultaneously and in parallel by PCR using appropriate cDNAs as templates. The primers used (SEQ ID NOS: 38-47) were appropriately designed so that they comprise a sequence complementary to a specific region of the cDNA of the relevant gene to be expressed as a protein, a complementary sequence to the stop codon, and GG residues at 5′-end to perform NcoI selection. Briefly, front primers must start with the first amino acid codon so that the reading frame coincides with that of the preceding GST, and the 5′-end nucleotides of front primers must not start with 5′-GG. Rear primers must contain a stop codon after the boundary of the presumed C terminal region of the relevant domain, and the 5′-end nucleotides of rear primers must start with 5′-GG. As a result, the PCR product amplified with these primers has an NcoI site (a site for the second restriction enzyme) generated only when it has been ligated to pGEX-4T3-PRESAT in the opposite orientation. This newly generated NcoI site is used in the subsequent selection step.
Any of the above-described genes is a 200-230 bp cDNA corresponding to a novel protein domain and encodes about 70 amino acid residues.
PCR amplification of a gene of interest was confirmed by electrophoresis. Then, the PCR product was ligated unpurified to pGEX-4T3-PRESAT vector, which was transformed into E. coli DH5a. The transformed DH5a was liquid cultured overnight without formation of single colonies. Next day, 1-3 μg of plasmid was purified from the resultant culture. This plasmid was digested with restriction enzyme NcoI and transformed into an expression host E. coli BL21 (DE3), which was then allowed to form single colonies. From the plates carrying single colonies, 3 single colonies for each of the genes were picked (3×5=15) and liquid cultured in LB medium. When OD reached about 0.5, IPTG was added to give a final concentration of 1 mM, and cells were cultured for another 4 hours. E. coli cells after completion of expression were harvested and sonicated. Then, the total cell was analyzed by SDS-PAGE, followed by confirmation of the band of the protein of interest (approx. 33-35 kD) on the gel (FIG. 4) (expression test). Of those colonies obtained, more than 90% of them (14/15) expressed a relevant fusion protein of interest with a predicted molecular weight, showing an extremely high efficiency.
Subsequently, disrupted cells derived from those colonies in which the expression of a fusion protein of interest with a predicted molecular weight had been confirmed were separated into solubilized fraction and insolubilized fraction by centrifugation. These two fractions and the total cell fraction were separately analyzed by SDS-PAGE to examine whether the fusion protein of interest was soluble or not (FIG. 5) (solubility test).
Also, GST activity measuring solution containing a mixture of 1-chloro-2,4-dinitrobenzene and glutathione was added to aliquots of solubilized fractions of proteins derived from those colonies in which expression of fusion proteins with predicted molecular weights had been confirmed to thereby start a reaction by GST, and determined the initial rate of the reaction by measuring the increase in UV absorbance at 350 nm with a spectrophotometer (FIG. 6) (CDNB assay). It was confirmed that the slopes of the straight lines in the graph are almost in proportion to the amount of relevant fusion protein of interest in the solubilized fraction, and thus it was found possible to carry out a semi-quantitative solubility test with a spectrophotometer.
Independently from the above test, the inventors picked 8 colonies from each plate, performing colony PCR and examined the ratio of plasmids from each clone comprising a gene of interest (i.e., efficiency of subcloning). As a result, it was confirmed that a gene with a correct length predicted from the target gene was integrated at the probability of 37/40 (92.5%).
Two clones were selected from those which were expressing a protein of a correct length, followed by determination and confirmation of the DNA sequences of the plasmids. It was confirmed that the sequences were completely correct and that they were in frame with GST.
The time period required for the entire process of the above operations was about 6 days, showing a significant reduction.
Example 3
Comparison of Efficiency between NcoI Selection and NdeI Selection
Comparative experiments were conducted to examine whether there would be any difference in efficiency between NcoI selection and NdeI selection in the preparation of expression systems for GST fusion proteins linked to protein fragments containing ubiquitin interacting motif (UIM).
A pair of primers for NcoI selection (SEQ ID NOS: 48 and 45) and a pair of primers for NdeI selection (SEQ ID NOS: 48 and 50) were used to amplify by PCR an approx. 200 bp fragment (the sequence of the coding strand is shown in SEQ ID NO: 51) of human Hrs gene comprising UIM sequence from human cDNA. The primers used were appropriately designed so that they comprise a sequence complementary to the cDNA of the relevant gene, a complementary sequence to the stop codon, and GG residues at 5′-end to perform NcoI selection. The primers for NdeI selection were appropriately designed in advance so that they comprise a complementary sequence to the stop codon and ATG residues at 5′-end. The above-described fragment is a 200 bp cDNA corresponding to a novel protein domain and encodes about 70 amino acid residues.
PCR amplification of the fragment was confirmed by electrophoresis. Then, the PCR product was ligated unpurified to dGST-T vector, which was transformed into E. coli .DH5a. The transformed DH5a was liquid cultured overnight without formation of single colonies. Next day, 1-3 μg of plasmid was purified from the resultant culture. This plasmid was digested with restriction enzyme NcoI or NdeI and transformed into an expression host E. coli BL21 (DE3), which was then allowed to form single colonies. Reaction conditions were as follows: 10 units of NcoI or 20 units of NdeI was used per 200 ng of plasmid, at 37° C., for 1 hour for both restriction enzymes. From the plates carrying single colonies, 3 single colonies for each were picked (3×5=15) and liquid cultured in LB medium. When OD reached about 0.5, IPTG was added to give a final concentration of 1 mM, and cells were cultured for another 4 hours (expression experiment). E. coli cells after completion of expression were harvested and sonicated. Then, the total cell, solubilized fraction and insolubilized fraction were analyzed by SDS-PAGE, followed by confirmation of the band of the fusion protein of interest (approx. 31 kD) on the gel. In the thus obtained colonies, the ratios of those colonies which expressed a fusion protein of interest with a predicted molecular weight were 14/15 when NcoI selection was used and 3/3 when NdeI selection was used, respectively. In both cases, the ratio was more than about 90% more than (14/15), showing extremely high efficiency.
Independently from the above experiment, the inventors picked several colonies from each plate, performing colony PCR and examined the ratio of plasmids in each clone comprising a gene of interest (i.e., efficiency of subcloning). As a result, it was confirmed that a gene with a correct length predicted from the target gene was integrated at the probability of 9/10 (90.0%) when NcoI selection was used and at the probability of 7/8 (88%) when NdeI selection was used; thus, the efficiency was almost equal.
From these experiments, it was found that both NcoI and NdeI may be used for the selection of ORF orientation.
Example 4
Method of Testing in a Short Period of Time the Expression Level in E. coli and Solubility of Fusion Proteins Prepared with dGST-T Vector (FIG. 7)
Using approx. 0.2 μg of mixture of the open circular vector prepared in Example 2 (which had human Vps4b gene integrated thereinto and underwent ORF selection by NcoI treatment), conditions for performing in a short period of time expression test and solubility test on the GST-Vps4 fusion protein (a gene of which was believed to have been constructed in that vector) were determined.
Briefly, approx. 0.2 μg of the pGEX-4T3-PRESAT comprising human Vsp4b gene and already linearized by NcoI treatment as described in Example 2 was transformed into an expression host E. coli BL21 (DE3), which was then allowed to form colonies on LB plate medium at 37° C. over 14 hours. Onto this plate, 200 μl of 0.1 M IPTG solution was sprayed. Colonies were grown further at 37° C. for 3 hours to thereby allow protein expression on the plate. To the E. coli colonies on the plate, 180 μl of 20 mM Tris-HCl buffer containing 0.15 M NaCl (pH 7.0)(hereinafter, called TBS buffer) was added to prepare suspension. The cells were sonicated to prepare the total cell fraction, solubilized fraction and insolubilized fraction, followed by analysis by SDS-PAGE in the same manner as in Example 2 (FIG. 8). The time required from the suspending of E. coli to analysis by SDS-PAGE was about 3 hours.
Like in Example 2, the band of the fusion protein of interest with a molecular weight of approx. 32 kDa was also confirmed in this method. It was revealed that the expression level and solubility of this protein were sufficient for subsequent experiments.
In this experiment, E. coli comprising a gene of the fusion protein of interest was subjected to expression test and solubility test as it was (i.e., as a mixture) without the step of single colony formation. However, as shown in Example 2, when ORF selection with NcoI has been performed, E. coli cells not comprising the gene of the fusion protein of interest are less than 10% of the E. coli cells forming colonies on the plate medium. Thus, it was found possible to judge the expression level and solubility by expression test and solubility test using electrophoresis.
The time period required for the entire process of the above operations is about 21 hours, showing a significant reduction. The time period required for the preceding steps from PCR to ORF selection with NcoI is 27 hours at the minimum. Thus, it was revealed that the entire process for constructing single protein and/or protein domain expression systems and performing solubility test can be done in 48 hours at the minimum.
The designations of the vectors prepared by the present inventors, the designations of commercial plasmids based on which the vectors were prepared, the designation of tags, first restriction enzymes, second restriction enzymes, linker sequences and references are summarized in the following Table.













TABLE IV






Designation of








commericial

First
Second



plasmid used

restriction
restriction
Linker


Designation of Vector
as a base
Designation of tag*
enzyme
enzyme
sequence
Reference







pGEX-4T3-PRESAT
pGEX-4T3
GST-thrombin
AhdI
NcoI
I
1, 7




cleavage site

NdeI


pGEX-3X-PRESAT
pGEX-3X
GST-Factor Xa
AhdI
NcoI
I
1, 7




cleavage site

NdeI


pET-Trx-PRESAT
pET-32a
TRX-His6-Factor
AhdI
KpnI
II
2, 3, 8




Xa cleavage site




(6xHis tag disclosed




as SEQ ID NO: 62)


pET-Hisx6-PRESAT
pET-32a
His6-Factor Xa
AhdI
KpnI
II
8


(6xHis tag disclosed as

cleavage site (6xHis


SEQ ID NO: 62)

tag disclosed as




SEQ ID NO: 62)


pET-FLAG-PRESAT
pET-32a
FLAG ®-
AhdI
AflII
III
4




Enterokinase




cleavage site


pET-LBT-PRESAT
pET-32a
LBT
AhdI
KpnI
II
5


pET-EGFP-PRESAT
pET-32a
EGFP-His6 (6xHis
AhdI
KpnI
II
6




tag disclosed as




SEQ ID NO: 62)





*Including the designation of tag and the designation of protease cleavage sequence when the tag and a protein of interest are cleaved.


Abbreviations


GST: glutathione-S-transferase (Schistosoma japonicum)


TRX: thioredoxin (E. coli)


His6: His-His-His-His-His-His (SEQ ID NO: 62)


LBT: lanthanide binding tag


FLAG (registered trademark): Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 63)


EGFP: enhanced green fluorescence protein (Aequorea victoria)






Linker Sequences (the underlined sequence is the AhdI restriction site)








I (487 bp) description: Trx gene and a part of


-PACAP artificial gene


(SEQ ID NO: 59)


GACCATTGGTCCACCTGACTGACGACAGTTTTGACACGGATGTACTCAAA


 


GCGGACGGGGCGATCCTCGTCGATTTCTGGGCAGAGTGGTGCGGTCCGTG


 


CAAAATGATCGCCCCGATTCTGGATGAAATCGCTGACGAATATCAGGGCA


 


AACTGACCGTTGCAAAACTGAACATCGATCAAAACCCTGGCACTGCGCCG


 


AAATATGGCATCCGTGGTATCCCGACTCTGCTGCTGTTCAAAAACGGTGA


 


AGTGGCGGCAACCAAAGTGGGTGCACTGTCTAAAGGTCAGTTGAAAGAGT


 


TCCTCGACGCTAACCTGGCCGGTTCTGGTTCTGGCCATATGGCTAGCCAT


 


CACCACCACCACCACAGCAGCGGCATTGACGGCCGGCATAGCGATGGCAT


 


CTTTACCGATAGCTATAGCCGCTATCGCAAACAGATGGCGGTGAAAAAGT


 


ATCTGGCGGCGGTGCTGGGCTAATAAGACCAAATGTC


 


II (110 bp) description: PACAP artificial gene


(SEQ ID NO: 60)


GACGGTCGGTCTAGCGATGGCATCTTTACCGATAGCTATAGCCGCTATCG


 


CAAACAGATGGCGGTGAAAAAGTATCTGGCGGCGGTGCTGGGCTAATAA


 


GACCAATGGTC


 


III (259 bp) description: human ubiquitin gene


(SEQ ID NO: 61)


GACGATAAGTCTCATATGCAGATTTTCGTGAAAACCCTGACCGGCAAAAC


 


CATCACCCTGGAAGTGGAACCGTCCGACACCATCGAAAACGTTAAAGCGA


 


AAATCCAGGACAAAGAAGGCATCCCGCCGGATCAGCAGCGTCTGATCTTC


 


GCGGGCAAACAGCTGGAAGACGGCCGTACCCTGTCCGATTACAACATCCA


 


GAAAGAATCTACCCTGCACCTGGTGCTGCGTCTGCGTGGCGGCTAATA


 


GACTTAAGGTC






REFERENCES


    1. Smith D B, Johnson K S. (1998) Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. Gene 67, 31-40
    2. LaVallie, E. R, DiBlasio, E. A, Kovacic, S, Grant, K. L, Schendel, P. F. and McCoy, J. M. (1993) A thioredoxin gene fusion expression system that circumvents inclusion body formation in the E. coli cytoplasm. Bio/Technology 11, 187-193
    3. Novy, R, Berg, J, Yaeger, K, and Mierendorf, R. (1995) inNovations 3, 7-9
    4. Hopp T P, Prickett K S, Price V, Libby R T, March C J, Cerretti P, Urdal D L, and Conlon P J. (1988) A Short Polypeptide Marker Sequence Useful for Recombinant Protein Identification and Purification. Biotechnology 6, 1205-1210
    5. Wohnert J, Franz K J, Nitz M, Imperiali B, Schwalbe H. (2003) Protein Alignment by a Coexpressed lanthanide-Binding Tag for the Measurement of Residual Dipor Couplings. J. Am. Chem. Soc. 125, 13338-13339
    6. Waldo G S, Standish B M, Berendzen J, Terwilliger T C. (1999) Rapid protein-folding assay using green fluorescent protein. Nat. Biotechnol. 17, 691-695.
    7. Goda N, Tenno T, Takasu H, Hiroaki H, and Shirakawa M. (2004) The PRESAT-vector: Asymmetric T-vector for high-throughput screening of soluble protein domains for structural proteomics. Protein Science 13, 652-658
    8. Tenno T, Goda N, Tateishi Y, Tochio H, Mishima M, Hayashi H, Shirakawa M, and Hiroaki H. (2004) High-throughput construction method for expression vector of peptides for NMR study suited for isotopic labeling. Protein Engineering, Design and Selection 17, 305-314


All the publications, patents and patent applications cited herein are incorporated herein by reference in their entity.
INDUSTRIAL APPLICABILITY
According to the present invention, it has become possible to greatly reduce the time required for the entire process of constructing protein and/or protein domain expression systems and performing solubility test.
Sequence Listing Free Text
<SEQ ID NO: 1>
SEQ ID NO: 1 shows the nucleotide sequence of sequence (I).
<SEQ ID NO: 2>
SEQ ID NO: 2 shows the nucleotide sequence of sequence (II).
<SEQ ID NO: 3>
SEQ ID NO: 3 shows the nucleotide sequence of sequence (III).
<SEQ ID NO: 4>
SEQ ID NO: 4 shows the nucleotide sequence of sequence (IV).
<SEQ ID NO: 5>
SEQ ID NO: 5 shows the nucleotide sequence of sequence (V)<
SEQ ID NO: 6>
SEQ ID NO: 6 shows the nucleotide sequence of sequence (VI).
<SEQ ID NO: 7>
SEQ ID NO: 7 shows the nucleotide sequence of sequence (VII).
<SEQ ID NO: 8>
SEQ ID NO: 8 shows the nucleotide sequence of sequence (VIII).
<SEQ ID NO: 9>
SEQ ID NO: 9 shows the nucleotide sequence of one example of sequence (IX) (when N1 has one base).
<SEQ ID NO: 10>
SEQ ID NO: 10 shows the nucleotide sequence of one example of sequence (X) (when N2 has one base).
<SEQ ID NO: 11>
SEQ ID NO: 11 shows the nucleotide sequence of one example of sequence (XI) (when N1 has one base).
<SEQ ID NO: 12>
SEQ ID NO: 12 shows the nucleotide sequence of one example of sequence (XII) (when N2 has one base).
<SEQ ID NO: 13>
SEQ ID NO: 13 shows the nucleotide sequence of one example of sequence (XIII) (when N1 has one base).
<SEQ ID NO: 14>
SEQ ID NO: 14 shows the nucleotide sequence of one example of sequence (XIV) (when N2 has one base).
<SEQ ID NO: 15>
SEQ ID NO: 15 shows the nucleotide sequence of one example of sequence (XV) (when N3 has one base).
<SEQ ID NO: 16>
SEQ ID NO: 16 shows the nucleotide sequence of one example of sequence (XVI) (when N4 has one base).
<SEQ ID NO: 17>
SEQ ID NO: 17 shows the nucleotide sequence of one example of sequence (XVII) (when N3 has one base).
<SEQ ID NO: 18>
SEQ ID NO: 18 shows the nucleotide sequence of one example of sequence (XVIII) (when N4 has one base).
<SEQ ID NO: 19>
SEQ ID NO: 19 shows the nucleotide sequence of one example of sequence (XIX) (when N3 has one base).
<SEQ ID NO: 20>
SEQ ID NO: 20 shows the nucleotide sequence of one example of sequence (XX) (when N4 has one base).
<SEQ ID NO: 21>
SEQ ID NO: 21 shows the sequence of the DNA used in site-directed mutagenesis of pGEX-4T3.
<SEQ ID NO: 22>
SEQ ID NO: 22 shows the nucleotide sequence of the front primer used in PCR reaction with pET32aPACAP as a template.
<SEQ ID NO: 23>
SEQ ID NO: 23 shows the nucleotide sequence of the rear primer used in PCR reaction with pET32aPACAP as a template.
<SEQ ID NO: 24>
SEQ ID NO: 24 shows the nucleotide sequence of the rear primer (for NcoI selection) used in PCR reaction with pET32aPACAP as a template.
<SEQ ID NO: 25>
SEQ ID NO: 25 shows the nucleotide sequence of one of the DNA strands of the approx. 500 bp PCR product described in Example 1. The other DNA strand was a complementary strand to this.
<SEQ ID NO: 26>
SEQ ID NO: 26 shows the nucleotide sequence of one of the two DNA strands which are the AhdI linker described in Example 1.
<SEQ ID NO: 27>
SEQ ID NO: 27 shows the nucleotide sequence of the other one of the two DNA strands which are the AhdI linker described in Example 1.
<SEQ ID NO: 28>
SEQ ID NO: 28 shows the nucleotide sequence of an approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (human SNX15a) to be used as a PCR template. Sequences added by primers are not included.
<SEQ ID NO: 29>
SEQ ID NO: 29 shows the amino acid sequence encoded by the approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (human SNX15a) to be used as a PCR template.
<SEQ ID NO: 30>
SEQ ID NO: 30 shows the nucleotide sequence of an approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (mouse SNX15a) to be used as a PCR template. Sequences added by primers are not included.
<SEQ ID NO: 31>
SEQ ID NO: 31 shows the amino acid sequence encoded by the approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (mouse SNX15a) to be used as a PCR template.
<SEQ ID NO: 32>
SEQ ID NO: 32 shows the nucleotide sequence of an approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (yeast Vps4) to be used as a PCR template. Sequences added by primers are not included.
<SEQ ID NO: 33>
SEQ ID NO: 33 shows the amino acid sequence encoded by the approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (yeast Vps4) to be used as a PCR template.
<SEQ ID NO: 34>
SEQ ID NO: 34 shows the nucleotide sequence of an approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (human Vps4b) to be used as a PCR template. Sequences added by primers are not included.
<SEQ ID NO: 35>
SEQ ID NO: 35 shows the amino acid sequence encoded by the approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (human Vps4b) to be used as a PCR template.
<SEQ ID NO: 36>
SEQ ID NO: 36 shows the nucleotide sequence of an approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (mouse Vps4b) to be used as a PCR template. Sequences added by primers are not included.
<SEQ ID NO: 37>
SEQ ID NO: 37 shows the amino acid sequence encoded by the approx. 220 bp fragment (coding strand) of MIT domain-comprising gene (mouse Vps4b) to be used as a PCR template.
<SEQ ID NO: 38>
SEQ ID NO: 38 shows the nucleotide sequence of a primer (HSS15F).
<SEQ ID NO: 39>
SEQ ID NO: 39 shows the nucleotide sequence of a primer (HSS15R).
<SEQ ID NO: 40>
SEQ ID NO: 40 shows the nucleotide sequence of a primer (MMS15F).
<SEQ ID NO: 41>
SEQ ID NO: 41 shows the nucleotide sequence of a primer (MMS15R).
<SEQ ID NO: 42>
SEQ ID NO: 42 shows the nucleotide sequence of a primer (ScVPS4F).
<SEQ ID NO: 43>
SEQ ID NO: 43 shows the nucleotide sequence of a primer (ScVPS4R).
<SEQ ID NO: 44>
SEQ ID NO: 44 shows the nucleotide sequence of a primer (HsVPS4F).
<SEQ ID NO: 45>
SEQ ID NO: 45 shows the nucleotide sequence of a primer (HsVPS4R).
<SEQ ID NO: 46>
SEQ ID NO: 46 shows the nucleotide sequence of a primer (MmVPS4F).
<SEQ ID NO: 47>
SEQ ID NO: 47 shows the nucleotide sequence of a primer (MmVPS4R).
Abbreviations: Sc: yeast; Hs: human; Mm: mouse; VPS4: VPS4; S15: SNX15
F: FORWARD; R: REVERSE
<SEQ ID NO: 48>
SEQ ID NO: 48 shows the nucleotide sequence of a primer (HrsF)
<SEQ ID NO: 49>
SEQ ID NO: 49 shows the nucleotide sequence of a primer for NcoI selection (HrsR-Nco).
<SEQ ID NO: 50>
SEQ ID NO: 50 shows the nucleotide sequence of a primer for NdeI selection (HrsR-Nde).
<SEQ ID NO: 51>
SEQ ID NO: 51 shows the nucleotide sequence of an approx. 200 bp fragment (coding strand) of UIM sequence-comprising human Hrs gene to be used as a PCR template. Sequences added by primers are not included.
<SEQ ID NO: 52>
SEQ ID NO: 52 shows the amino acid sequence encoded by the approx. 200 bp fragment (coding strand) of UIM sequence-comprising human Hrs gene to be used as a PCR template.
<SEQ ID NO: 53>
SEQ ID NO: 53 shows the nucleotide sequence of a primer corresponding to the C-terminal of ORF (the protein domain of interest does not include a stop codon) when the first restriction enzyme is AhdI and the second restriction enzyme is NcoI.
<SEQ ID NO: 54>
SEQ ID NO: 54 shows the nucleotide sequence of a primer corresponding to the C-terminal of ORF (the protein domain of interest does not include a stop codon) when the first restriction enzyme is AhdI and the second restriction enzyme is NdeI.
<SEQ ID NO: 55>
SEQ ID NO: 55 shows one example of the nucleotide sequence of N1 in sequences (IX) to (XIV).
<SEQ ID NO: 56>
SEQ ID NO: 56 shows one example of the nucleotide sequence of N2 in sequences (IX) to (XIV).
<SEQ ID NO: 57>
SEQ ID NO: 57 shows one example of the nucleotide sequence of N3 in sequences (XV) to (XX).
<SEQ ID NO: 58>
SEQ ID NO: 58 shows one example of the nucleotide sequence of N4 in sequences (XV) to (XX).
<SEQ ID NO: 59>
SEQ ID NO: 59 shows the nucleotide sequence of linker I.
<SEQ ID NO: 60>
SEQ ID NO: 60 shows the nucleotide sequence of linker II.
<SEQ ID NO: 61>
SEQ ID NO: 61 shows the nucleotide sequence of linker III.

## Claims

1. A vector comprising:
two first restriction enzyme recognition sequences different in nucleotide sequence both of which are recognized by a first restriction enzyme,
wherein one of the first restriction enzyme recognition sequences comprises a part of a second restriction enzyme recognition sequence which is recognized by a second restriction enzyme that is different from the first restriction enzyme, and the other one of the first restriction enzyme recognition sequences does not comprise the part of the second restriction enzyme recognition sequence which is recognized by the second restriction enzyme; and
a coding region of a specific protein for expressing a fusion protein which includes a protein and/or a protein domain encoded by a foreign gene and the specific protein linked to the protein and/or the protein domain,
wherein the two first restriction enzyme recognition sequences different in nucleotide sequence are provided downstream of the coding region of the specific protein, one of said first restriction enzyme recognition sequences comprising the part of the second restriction enzyme recognition sequence is located proximal to the coding region of the specific protein, and the other first restriction enzyme recognition sequence not comprising said part of the second restriction enzyme recognition sequence is located distal to the coding region of the specific protein.

2. The vector according to claim 1, wherein the first restriction enzyme is a restriction enzyme which produces a 3′-overhang at the end of the DNA fragments it digested.

3. The vector according to claim 2, wherein the base at the 3′-overhang is thymine.

4. The vector according to claim 1, wherein the first restriction enzyme is selected from the group consisting of AhdI or an isoschizomer thereof, XcmI or an isoschizomer thereof, or a combination thereof.

5. The vector according to claim 4, wherein the first restriction enzyme is selected from the group consisting of AhdI or an isoschizomer thereof, or a combination thereof, and the second restriction enzyme is selected from the group consisting of NcoI, DsaI, EcoTI41, NdeI, SfeI, AvaI, SmII, XhoI, PstI, EcoT221, PshBI, AccI, ApaLI, Psil, ScaI, SpII, Bsp107I, Bsp1286I, BspT107I, Bsp1407I, TatI, HgiCI, KpnI, SpeI, BlnI, NheI, XbaI: SspI, EcoRV and isoschizomers thereof.

6. The vector according to claim 1, wherein the two first restriction enzyme recognition sequences different in nucleotide sequence both of which are recognized by the first restriction enzyme are inserted into its multicloning site.

7. The vector according to claim 1, wherein the vector comprises a coding region of glutathione-S-transferase for expressing a protein and/or a protein domain encoded by a foreign gene in the form of a fusion protein linked to glutathione-S-transferase when the foreign gene is integrated in the vector.

8. The vector according to claim 7, wherein glutathione-S-transferase is isolated from a mammal, Schistosoma japonicum or Escherichia coli.

9. An open circular vector comprising a double-stranded DNA, which is obtained by treating the vector according to claim 1 with the first restriction enzyme.

10. A method of preparing a vector, comprising:
introducing into a multicloning site of a plasmid, phage, cosmid, PI vector, bacterial artificial chromosome vector or yeast artificial chromosome vector a double-stranded DNA comprising two first restriction enzyme recognition sequences different in nucleotide sequence both of which are recognized by a first restriction enzyme,
wherein one of the first restriction enzyme recognition sequences comprises a part of a second restriction enzyme recognition sequence which is recognized by a second restriction enzyme that is different from the first restriction enzyme, and the other one of the first restriction enzyme recognition sequences does not comprise said part of the second restriction enzyme recognition sequence which is recognized by the second restriction enzyme;
reacting the first restriction enzyme recognition sequences with the first restriction enzyme to expose the part of the second restriction enzyme recognition sequence contained in the first restriction enzyme recognition sequence: and
attaching the part of the second restriction enzyme recognition sequence to a foreign gene, which is configured to complete the second restriction enzyme recognition sequence if inserted in one orientation but not complete the second restriction enzyme recognition sequence if inserted in the opposite orientation.

11. A double-stranded DNA prepared by a process comprising:
reacting the vector according to claim 1 with the first restriction enzyme to expose the part of the second restriction enzyme recognition sequence contained in the first restriction enzyme recognition sequence.

12. A method of preparing a protein and/or a protein domain encoded by a foreign gene, comprising:
introducing into a vector a double-stranded DNA comprising two first restriction enzyme recognition sequences different in nucleotide sequence both of which are recognized by a first restriction enzyme,
wherein one of the first restriction enzyme recognition sequences comprises a part of a second restriction enzyme recognition sequence which is recognized by a second restriction enzyme that is different from the first restriction enzyme, and the other one of the first restriction enzyme recognition sequences does not comprise said part of the second restriction enzyme recognition sequence which is recognized by the second restriction enzyme;
reacting the first restriction enzyme recognition sequences with the first restriction enzyme to expose the part of the second restriction enzyme recognition sequence contained in the first restriction enzyme recognition sequence;
attaching the part of the second restriction enzyme recognition sequence to the foreign gene, which is configured to complete the second restriction enzyme recognition sequence if inserted in one orientation but not complete the second restriction enzyme recognition sequence if inserted in the opposite orientation;
applying the second restriction enzyme to the vector,
wherein when the foreign gene is so oriented to ligate to not produce the second restriction enzyme recognition sequence recognized by the second restriction enzyme, the second restriction enzyme does not digest the vector, and the vector is not linearized and remains circular; but when the foreign gene is so reversibly oriented to ligate to complete the second restriction enzyme recognition sequence recognized by the second restriction enzyme, the second restriction enzyme digests to linearize the vector; and
selecting the vector that is unlinearized by transforming a bacterial cell with the vector that remains circular.